Ligands to radiation-induced molecules

ABSTRACT

A method for identifying a molecule that binds an irradiated tumor in a subject and molecules identified thereby. In some embodiments, the method includes the steps of (a) exposing a tumor to ionizing radiation; (b) administering to a subject a library of diverse molecules; and (c) isolating from the tumor one or more molecules of the library of diverse molecules, whereby a molecule that binds an irradiated tumor is identified. Also provided are targeting ligands that bind an irradiated tumor and therapeutic and diagnostic methods that employ the disclosed targeting ligands.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. patent applicationSer. No. 11/183,325, filed Jul. 15, 2005, which itself is acontinuation-in-part of U.S. patent application Ser. No. 10/259,087,filed Sep. 27, 2002, which is based on and claims priority to U.S.Provisional Patent Application Ser. No. 60/328,123, filed Oct. 3, 2001.This application is also a continuation-in-part of U.S. patentapplication Ser. No. 10/689,006, filed Oct. 20, 2003, which itself is acontinuation-in-part of U.S. patent application Ser. No. 09/914,605,filed Aug. 30, 2001, now U.S. Pat. No. 7,049,140, and U.S. patentapplication Ser. No. 10/259,087, filed Sep. 27, 2002. The entiredisclosures of this U.S. patent and these patent applications are hereinincorporated by reference in their entireties.

GRANT STATEMENT

This work was supported by grants CA58508, CA70937, CA89888, CA89674,and CA90949 from the U.S. National Institutes of Health. Thus, the U.S.government has certain rights in the presently disclosed subject matter.

TECHNICAL FIELD

The presently disclosed subject matter generally relates to ligands forradiation guided delivery of an active agent. The presently disclosedsubject matter also provides new radiation-induced neoantigens that canbe targeted by targeting ligands that specifically bind an irradiatedtumor. Also provided are therapeutic and diagnostic uses for the same.

BACKGROUND

Tumor-specific drug delivery has the potential to minimize toxicity tonormal tissues and improve the bioavailability of therapeutic agents totumor cells (Hallahan at al., 1995b; Arap et al., 1998). Targetingligands include antibodies and peptides that accumulate in tumors byspecific binding to target molecules present on tumor vasculature,endothelial cells associated with tumor vasculature, and tumor cells.Effective target molecules are generally cell surface receptors or othermolecules present at the exterior of tumor cells such that they areaccessible to targeting ligands (Hallahan et al., 2001a).

Existing site-specific drug delivery systems include ligands thatrecognize a tumor marker such as Her2/neu (v-erb-b2 avian erythroblasticleukemia viral oncogene homologue 2), CEA (carcinoembryonic antigen; Itoet al., 1991), and breast cancer antigens (Manome et al., 1994; Kirpotinof al., 1997; Becerril et al., 1999). See also PCT InternationalPublication No. WO 98/10795. In an effort to identify ligands that arecapable of targeting to multiple tumor types, targeting ligands havebeen developed that bind to target molecules present on tumorvasculature (Baillie et al., 1995; Pasqualini & Ruoslahti, 1996; Arap etal., 1998; Burg et al., 1999; Ellerby et al., 1999).

Despite these advances, current methods for targeted drug delivery arehindered by targeting ligands that also bind normal tissues and/or alack of targeting ligands that bind multiple tumor types. Ideally, atargeting molecule should display specific targeting in the absence ofsubstantial binding to normal tissues, and a capacity for targeting to avariety of tumor types and stages. Thus, there exists a long-felt needin the art for methods and compositions to achieve site-specific,tumoral delivery of therapeutic and/or diagnostic agents.

To meet this need, the presently disclosed subject matter providesmethods for identifying ligands that bind to irradiated tumors, andligands that have been bind irradiated tumors and tissues. Such ligandsare useful for guided drug delivery (e.g., radiation guided drugdelivery), among other applications.

SUMMARY

This Summary lists several embodiments of the presently disclosedsubject matter, and in many cases lists variations and permutations ofthese embodiments. This Summary is merely exemplary of the numerous andvaried embodiments. Mention of one or more representative features of agiven embodiment is likewise exemplary. Such an embodiment can typicallyexist with or without the feature(s) mentioned; likewise, those featurescan be applied to other embodiments of the presently disclosed subjectmatter, whether listed in this Summary or not. To avoid excessiverepetition, this Summary does not list or suggest all possiblecombinations of such features.

The presently disclosed subject matter provides compositions forradiation-guided targeting. In some embodiments, the compositionscomprise one or more targeting ligands that bind to a TIP-1 polypeptide.In some embodiments, the one or more targeting ligands comprises apeptide or an antibody or derivative thereof that binds to the TIP-1polypeptide. In some embodiments, the peptide that binds to TIP-1comprises an amino acid sequence as set forth in SEQ ID NOs: 1, 35,71-76, and 78-86. In some embodiments, the antibody or derivativethereof that binds to TIP-1 is selected from among polyclonalantibodies, monoclonal antibodies, scFv antibodies, and antibodyfragments that bind to TIP-1. In some embodiments, the antibody orderivative thereof that binds to TIP-1 is humanized. In someembodiments, the one or more targeting ligands bind to one or more tumortypes selected from among an irradiated glioma, a melanoma, a lungcarcinoma, and a prostate carcinoma. In some embodiments, thecomposition further comprises a detectable label, a therapeutic agent, adrug carrier, or combinations thereof. In some embodiments, thedetectable label is an in vivo detectable label that can be detectedusing magnetic resonance imaging, scintigraphic imaging, ultrasound, orfluorescence. In some embodiments, the in vivo detectable labelcomprises a radionuclide label selected from the group consisting of¹³¹I or ^(99m)Tc. In some embodiments, the therapeutic agent is selectedfrom the group consisting of a radionuclide, a cytotoxin, a therapeuticgene, and a chemotherapeutic agent. In some embodiments, the drugcarrier is selected from the group consisting of a viral vector, aliposome, a plasmid, a microcapsule, and combinations thereof.

The presently disclosed subject matter also provides methods fordetecting a tumor in a subject. In some embodiments, the presentlydisclosed methods comprise (a) exposing a target areas of the subjectwhere the presence of a tumor is suspected to ionizing radiation; (b)administering to the subject a composition comprising one or moretargeting ligands conjugated to a detectable label, wherein the one ormore targeting ligands bind to a TIP-1 polypeptide; and (c) detectingthe detectable label to thereby detect the tumor. In some embodiments,the one or more targeting ligands comprises a peptide or an antibody orderivative thereof that binds to the TIP-1 polypeptide. In someembodiments, the peptide that binds to TIP-1 comprises an amino acidsequence as set forth in SEQ ID NOs: 1, 35, 71-76, and 78-86. In someembodiments, the antibody or derivative thereof that binds to TIP-1 isselected from among polyclonal antibodies, monoclonal antibodies, scFvantibodies, and antibody fragments that bind to TIP-1. In someembodiments, the antibody or derivative thereof that binds to TIP-1 ishumanized. In some embodiments, the exposing comprises exposing thetumor to less than about 2 Gy ionizing radiation. In some embodiments,the exposing comprises exposing the tumor to at least about 2 Gyionizing radiation. In some embodiments, the exposing comprises exposingthe tumor to about 10 Gy to about 20 Gy ionizing radiation. In someembodiments, the administering comprises administering the targetingligand by intravascular provision. In some embodiments, theadministering comprises administering the targeting ligand subsequent toradiation exposure. In some embodiments, the administering comprisesadministering the targeting ligand 0 hours to about 24 hours followingradiation exposure. In some embodiments, the administering comprisesadministering the targeting ligand about 4 hours to about 24 hoursfollowing radiation exposure. In some embodiments, the subject is awarm-blooded vertebrate. In some embodiments, the detecting comprisesdetecting the radionuclide label using positron emission tomography,single photon emission computed tomography, gamma camera imaging, orrectilinear scanning. In some embodiments, the tumor comprises a tumorselected from the group consisting of bladder carcinoma, breastcarcinoma, cervical carcinoma, cholangiocarcinoma, colorectal carcinoma,gastric sarcoma, glioma, lung carcinoma, lymphoma, melanoma, multiplemyeloma, osteosarcoma, ovarian carcinoma, pancreatic carcinoma, prostatecarcinoma, stomach carcinoma, a head, a neck tumor, and a solid tumor.In some embodiments, the tumor is selected from the group consisting ofa glioma, a melanoma, a lung carcinoma, and a prostate carcinoma.

In some embodiments, the presently disclosed methods further comprisesimultaneously detecting two or more tumors in the subject. In someembodiments, the two or more tumors in a subject comprise two or moretumor types.

The presently disclosed subject matter also provides methods forradiation-guided delivery of a composition comprising an active agent toa target tissue in a subject. In some embodiments, the presentlydisclosed methods comprise (a) exposing the target tissue to ionizingradiation; and (b) administering to the subject a therapeuticcomposition, a diagnostic composition, or a combination thereof, whereinthe therapeutic composition, diagnostic composition, or the combinationthereof comprises a composition comprising one or more targeting ligandsthat bind to a TIP-1 polypeptide, whereby the composition comprising anactive agent is selectively targeted to the target tissue. In someembodiments, the active agent comprises a therapeutic agent, adiagnostic agent, or a combination thereof. In some embodiments, thetarget tissue comprises a tumor, tumor vasculature, or a combinationthereof. In some embodiments, the one or more targeting ligandscomprises a peptide or an antibody or derivative thereof that binds tothe TIP-1 polypeptide. In some embodiments, the peptide that binds toTIP-1 comprises an amino acid sequence as set forth in SEQ ID NOs: 1,35, 71-76, and 78-86. In some embodiments, the antibody or derivativethereof that binds to TIP-1 is selected from among polyclonalantibodies, monoclonal antibodies, scFv antibodies, and antibodyfragments that bind to TIP-1. In some embodiments, the antibody orderivative thereof that binds to TIP-1 is humanized. In someembodiments, the tumor is a primary or a metastasized tumor. In someembodiments, the tumor is selected from a tumor selected from the groupconsisting of bladder carcinoma, breast carcinoma, cervical carcinoma,cholangiocarcinoma, colorectal carcinoma, gastric sarcoma, glioma, lungcarcinoma, lymphoma, melanoma, multiple myeloma, osteosarcoma, ovariancarcinoma, pancreatic carcinoma, prostate carcinoma, stomach carcinoma,a head tumor, a neck tumor, and a solid tumor. In some embodiments, thetumor is selected from the group consisting of a glioma, a melanoma, alung carcinoma, and a prostate carcinoma. In some embodiments, theexposing comprises exposing the tumor to at least about 2 Gy ionizingradiation. In some embodiments, the administering comprisesadministering the targeting ligand by intravascular provision. In someembodiments, the administering comprises administering the targetingligand subsequent to radiation exposure. In some embodiments, theadministering comprises administering the targeting ligand 0 hours toabout 24 hours following radiation exposure. In some embodiments, thesubject is a warm-blooded vertebrate.

The presently disclosed subject matter also provides methods forscreening a plurality of potential ligands for an ability to bind to aradiation-induced TIP-1 neoantigen present on a cell. In someembodiments, the presently disclosed methods comprise (a) contacting thecell with a first solution, the first solution comprising the pluralityof potential ligands; (b) isolating a second solution, the secondsolution comprising those potential ligands that do not bind to thecell; (c) removing any potential ligands bound to the cell; (d) treatingthe cell with radiation, wherein the treating results in aradiation-induced TIP-1 neoantigen being present on the cell; (e)contacting the cell with the second solution; and (f) detecting bindingof a potential ligand to the radiation-induced TIP-1 neoantigen on thecell. In some embodiments, the plurality of potential ligands comprisesa plurality of recombinant peptides, a plurality of antibodies orfragments or derivatives thereof, or combinations thereof. In someembodiments, the plurality of antibodies or fragments or derivativesthereof comprises a plurality of phage-displayed antibodies or fragmentsor derivatives thereof. In some embodiments, the plurality ofphage-displayed antibodies or fragments or derivatives thereof comprisesa plurality of phage-displayed single chain variable fragment (scFv)antibodies, a plurality of phage-displayed Fab fragments, orcombinations thereof. In some embodiments, the phage-displayedantibodies are humanized. In some embodiments, one or more of thephage-displayed antibodies further comprises an epitope tag. In someembodiments, the epitope tag is selected from the group consisting of ac-myc tag and a histidine tag. In some embodiments, the plurality ofpeptides comprises a plurality of peptides of from 4 to 50 amino acidsin length. In some embodiments, the plurality of peptides comprises aplurality of peptides of from 7 to 50 amino acids in length. In someembodiments, the plurality of peptides comprises a plurality of peptidescomprising the amino acid sequence HVGGSSV (SEQ ID NO: 35). In someembodiments, the cell is selected from the group consisting of a tumorcell and a vascular endothelial cell. In some embodiments, the vascularendothelial cell is present within tumor microvasculature. In someembodiments, the detecting is by a technique selected from ELISA,BIACORE, Western blotting, immunohistochemistry, fluorometricmicrovolume assay technology, mass spectroscopy, MALDI-MS, andMALDI-TOF.

Accordingly, it is an object of the presently disclosed subject matterto provide novel targeting ligands that bind irradiated tumors andtherapeutic and/or diagnostic methods using the same. This and othersobjects are achieved in whole or in part by the presently disclosedsubject matter.

An object of the presently disclosed subject matter having been statedabove, other objects and advantages of the presently disclosed subjectmatter will become apparent to those skilled in the art after a study ofthe following description and non-limiting Examples.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic depicting a polyvalent immunoconjugate. In thisFigure, the polyvalent immunoconjugate comprises nanoparticle to whichtwo antibodies (Antibody 1 and Antibody 2) and one therapeutic agent (inthis case, a gamma emitter) are complexed.

FIG. 2 are graphs depicting the results of binding competition of anscFv antibody that binds to TIP-1 (TIP1-E11) to a purified TIP-GSTfusion protein with a selective synthetic biotinylated peptide(HGDPNHVGGSSV; SEQ ID NO: 71) derived from random peptide library asdetermined by ELISA under different conditions. The top panel is a graphdepicting the results of the binding competition between the TIP1-E11scFv antibody (diamonds) and TIP-1 in the presence of differentdilutions of a competitor peptide having the amino acid sequence HVGGSSV(SEQ ID NO: 35) (squares). The bottom panel is a graph depicting theresults of the binding competition between the TIP1-E11 scFv antibody(triangles) and TIP-1 in the presence of different dilutions of acompetitor peptide having the amino acid sequence HVGGSSV (SEQ ID NO:35) (crosses) in the presence or absence of guinea pig serum (diamonds)or mouse (squares) serum.

FIGS. 3A and 3B depict the results of TIP-1 immunohistochemical stainingof tumor sections. Tumors were treated with 0 Gy (FIG. 3A) or 3 Gy (FIG.3B), resected and fixed at 6 hours after irradiation. Tumors weresectioned and stained with polyclonal rabbit anti-mouse antibody toTIP-1. Sections were then stained by use of Secondary antibodyconjugated to HRP. Shown are depictions of microscopic photographs using100× objectives.

FIG. 4 depicts a western blot for TIP-1 protein separated by PAGE,transferred, and incubated with polyclonal antibody to TIP-1. Depictedare autoradiographs of TIP-1 protein at 1, 4, and 24 hours afterirradiation with 3 Gy compared to TIP-1 protein in untreated controls (0Gy).

FIGS. 5A-5C depict NIR imaging of labeled HGDPNHVGGSSV (SEQ ID NO: 71)binding in irradiated orthotopic prostate cancers.

FIG. 5A presents a transgenic prostate tumor. FIG. 5B presents the PC3tumor implanted into the prostate of nude mice. FIG. 5C presents thenegative control scrambled peptide administered to a mouse bearingirradiated PC3 orthotopic tumor. All mice were treated with 3 Gy. Thearrow in FIG. 5C indicates the location of the orthotopic prostatetumor.

FIGS. 6A and 6B depict NIR images demonstrating the specificity of tumorbinding by phage peptides. FIGS. 6A and 6B depict NIR images of phagedisplayed RGDGSSV (SEQ ID NO: 75) and HGDPNHVGGSSV (SEQ ID NO: 71) inmice bearing irradiated tumors in the left hind limb and untreatedcontrol tumor in right leg.

FIG. 7 is a bar graph showing the percentage of total emission that islocalized to the tumors using different phage peptides (HSVGGSSV—SEQ IDNO: 35; RGD; and HGSSV—SEQ ID NO: 76). The gray bars show the percentageof Cy7 labeled phage binding within irradiated tumor. The black barsshow the percentage of Cy 7 labeled phage binding within the untreated(0 Gy) control tumor in the opposite hind limb. Data were collected whenphage were cleared from the circulation. Bars labeled “other” show themaximal tumor specific binding of all other phage.

FIG. 8 depicts NIR images using Xenogen imaging system of Cy 7 labeledHGDPNHVGGSSV (SEQ ID NO: 71) phage. Depictions of representativephotographs of the same mouse from days 1, 3, 7 and 9, following 3 Gyx-irradiation and HGDPNHVGGSSV phage (SEQ ID NO: 71) are shown. The redarrows indicate the jugular catheter injection site of labeled phage.Red and yellow color intensity areas are the highest areas ofillumination. Color intensity is overlaid upon photographs of the nudemouse within the Xenogen imaging system.

FIG. 9 is two graphs depicting the pharmacokinetics of the phage bindingin tumors. The percentage of phage binding in tumor and of the rest ofthe entire body are shown for HGDPNHVGGSSV (SEQ ID NO: 71) phage (leftpanel) and RGDGSSV (SEQ ID NO: 75) page (right panel). Data wereacquired from the Xenogen imaging system using images as shown in FIG.8. The percentage of labeled phage binding in tumor is shown in thedotted line and the percentage of phage in the rest of the body is shownas a solid line over the course of several days.

FIGS. 10A-10D are images of immunohistochemistry of phage antibodystaining of tumor sections acquired from mice shown in FIG. 8. Thetumors from mice treated with 3 Gy-irradiation and phage were fixed at 4hours (10B) and 7 days (10C & 10D) after administration of phage.

Tumors were sectioned and stained with H & E and antibody that isspecific for phage. Brown staining indicates phage binding.

FIGS. 11A-11C are images depicting fluorescence-labeled HGDPNHVGGSSV(SEQ ID NO: 71) peptide within micro-vasculature of irradiated tumors.The mouse bearing an irradiated PC3 tumor was irradiated andCy7-labeled. HGDPNHVGGSSV (SEQ ID NO: 71) was injected. NIR imagingshows that the peptide binds within tumor (arrow). Texas red-labeledpeptide was injected after treatment with 3 Gy. Shown is fluorescencemicroscopy on the right and the same stained section (FIG. 11B).

FIG. 12 is a schematic and images showing the HGDPNHVGGSSV (SEQ ID NO:71) peptide was bound to strepavidiin by use of the biotin on a linkerpolyglycine. The streptavidin is labeled with Cy7. The Cy7 labeledstreptavidin-peptide complexes injected by jugular vein into tumorbearing mice. The panel on the left shows the distribution of peptide inuntreated mouse. The panel on the right shows distribution of peptidebinding following irradiation of hind limb tumors.

FIG. 13 is a set of images showing orthotopic glioblastoma tumors in thebrains of mice are shown on the left. The H460 lung cancer in the thoraxof the mouse and colon cancer is on the right. Mice on the right aretreated with radiation. The mouse on the far left is the untreatedcontrol mouse. The Cy7 labeled strepavidin-HGDPNHVGGSSV (SEQ ID NO: 71)complex was injected by tail vein. Mice were imaged using NIR and theXenogen IVIS system. Shown is NIR imaging at 48 hours after injection.The arrow indicates no peptide binding to irradiated liver.

FIGS. 14A-14C are a set of images showing PC3 tumor implanted into theprostate of nude mice (FIGS. 14A and 14B) and the transgenic PTENprostate tumor (FIG. 14C). All mice were treated with 3 Gy. FIG. 14B isthe negative control peptide administered to mouse bearing irradiatedPC3 orthotopic tumor. The arrow indicates the location of the orthotopicprostate tumor shown below. Cy7-labeled HVGGSSV (SEQ ID NO: 35) peptidewas imaged by the Xenogen system.

FIGS. 15A and 15B are imaging showing orthotopic PC3 tumor in the nudemouse. In FIG. 15A, the mouse imaged in FIG. 14A was euthanized andprostate tumor was identified, (Arrow). In FIG. 15B, clockwise: prostatetumor, heart, liver & lung were then resected and imaged by NIR usingthe Xenogen system.

FIGS. 16A-16C are images showing prostate and seminal vesicles in theprostate-specific conditional PTEN transgenic. FIG. 16A) The mouseimaged in FIG. 14C was euthanized and prostate tumor was identified,(Arrow). FIG. 16B) Clockwise: prostate tumor, heart, liver & lung werethen resected and imaged by NIR using Xenogen imaging system.

FIGS. 17A-17C are images showing Fluorescent confocal microscopy ofHGDPNHVGGSSV (SEQ ID NO: 71)-strepavidin. FIG. 17A) HUVEC 0 Gy controlcells. FIG. 17B) 4 hours following irradiation 3 Gy. FIG. 17C)HGDPNHVGGSSV (SEQ ID NO: 71) strepavidin incubation for 24 hours after 3Gy.

DETAILED DESCRIPTION I. Definitions

While the following terms are believed to be well understood by one ofordinary skill in the art, the following definitions are set forth tofacilitate explanation of the presently disclosed subject matter.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which the presently disclosed subject matter belongs.Although any methods, devices, and materials similar or equivalent tothose described herein can be used in the practice or testing of thepresently disclosed subject matter, representative methods, devices, andmaterials are now described.

Following long-standing patent law convention, the terms “a”, “an”, and“the” refer to “one or more” when used in this application, includingthe claims. Thus, for example, reference to “a cell” (e.g., “a PEP”)includes a plurality of such cells (e.g., a plurality of PEPs), and soforth.

Unless otherwise indicated, all numbers expressing quantities ofingredients, reaction conditions, and so forth used in the specificationand claims are to be understood as being modified in all instances bythe term “about”. Accordingly, unless indicated to the contrary, thenumerical parameters set forth in this specification and attached claimsare approximations that can vary depending upon the desired propertiessought to be obtained by the presently disclosed subject matter.

As used herein, the term “about,” when referring to a value or to anamount of mass, weight, time, volume, concentration or percentage ismeant to encompass variations of in some embodiments ±20%, in someembodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, insome embodiments ±0.5%, and in some embodiments ±0.1% from the specifiedamount, as such variations are appropriate to perform the disclosedmethods or employ the disclosed compositions.

As used herein, the term “cell” refers not only to the particularsubject cell (e.g., a living biological cell), but also to the progenyor potential progeny of such a cell. Because certain modifications canoccur in succeeding generations due to either mutation or environmentalinfluences, such progeny might not, in fact, be identical to the parentcell, but are still included within the scope of the term as usedherein.

The term “ligand” as used herein refers to a molecule or other chemicalentity having a capacity for binding to a target. A ligand can comprisea peptide, an oligomer, a nucleic acid (e.g., an aptamer), a smallmolecule (e.g., a chemical compound), an antibody or fragment thereof, anucleic acid-protein fusion, and/or any other affinity agent.

The term “small molecule” as used herein refers to a compound, forexample an organic compound, with a molecular weight in some embodimentsof less than about 1,000 daltons, in some embodiments less than about750 daltons, in some embodiments less than about 600 daltons, and insome embodiments less than about 500 daltons. A small molecule also hasa computed log octanol-water partition coefficient in some embodimentsin the range of about −4 to about +14, and in some embodiments in therange of about −2 to about +7.5.

The term “target tissue” as used herein refers to an intended site foraccumulation of a ligand following administration to a subject. Forexample, the methods disclosed herein can employ a target tissuecomprising an irradiated tumor.

The term “control tissue” as used herein refers to a site suspected tosubstantially lack binding and/or accumulation of an administeredligand. For example, in accordance with the methods of the presentlydisclosed subject matter, a non-irradiated tumor and a non-canceroustissue are control tissues.

The terms “target” or “target molecule” as used herein each refer to anysubstance that is specifically bound by a ligand. Thus, the term “targetmolecule” encompasses macromolecules including but not limited toproteins, nucleic acids, carbohydrates, lipids, and complexes thereof.

As used herein, the terms “radiation-induced target”, “radiation-inducedtumor target”, and “radiation-induced neoantigen” refer to a targetmolecule in a tumor whose expression, localization, or ligand-bindingcapacity is induced by radiation. Such a target molecule can comprise amolecule at the surface of a tumor cell, within a tumor cell, or in theextracellular matrix surrounding a tumor cell. Alternatively, a targetmolecule can comprise a molecule present at the surface of or within avascular endothelial cell, or at the surface of or within a bloodcomponent such as a platelet or a leukocyte. In some embodiments, aradiation-induced neoantigen is selected from the group consisting ofP-selectin, E-selectin, Endoglin, α_(2b)β₃ integrin, α_(v)β₃ integrin,and TIP-1.

In some embodiments, a radiation-induced neoantigen comprises is a TIP-1polypeptide. TIP-1 is also known as T-cell leukemia virus type I bindingprotein 3 (TAX1BP3), and several nucleic acid and amino acid sequencesfor TIP-1 orthologs from various species are available in the GENBANK®database. For example, TIP-1 sequences that are disclosed in theGENBANK® database include, but are not limited to TIP-1 nucleic acid andamino acid sequences from human (NM_(—)014604 and NP_(—)055419), mouse(NM_(—)029564 and NP_(—)083840), rat (NM_(—)001025419 andNP_(—)001020590), bovine (BC102510 and NP_(—)001029646), and Xenopus(BC063221 and NP_(—)989230).

The term “induce”, as used herein to refer to changes resulting fromradiation exposure, encompasses activation of gene transcription orregulated release of proteins from cellular storage reservoirs tovascular endothelium. Alternatively, induction can refer to a process ofconformational change, also called activation, such as that displayed bythe glycoprotein IIb/IIIa integrin receptor upon radiation exposure(Staba et al., 2000; Hallahan et al., 2001a). See also U.S. Pat. No.6,159,443. Additional proteins undergo conformational changes inresponse to radiation or other stimuli (e.g., co-culture with tumorcells), and these conformational change are also intended to beencompassed by the term “induction”. An exemplary protein that undergoesconformational changes in response to co-culture with tumor cells and/orexposure to radiation is perlecan (GENBANK® Accession Nos. P98160 andNP_(—)005520).

The terms “targeting” or “homing”, as used herein to describe the invivo activity of a ligand following administration to a subject, eachrefer to the preferential movement and/or accumulation of a ligand in atarget tissue as compared with a control tissue.

The terms “selective targeting” of “selective homing” as used hereineach refer to a preferential localization of a ligand that results in anamount of ligand in a target tissue that is in some embodiments about2-fold greater than an amount of ligand in a control tissue, in someembodiments about 5-fold or greater than an amount of ligand in acontrol tissue, and in some embodiments an amount that is about 10-foldor greater than an amount of ligand in a control tissue. The terms“selective targeting” and “selective homing” also refer to binding oraccumulation of a ligand in a target tissue concomitant with an absenceof targeting to a control tissue, in some embodiments the absence oftargeting to all control tissues.

The term “absence of targeting” is used herein to describe substantiallyno binding or accumulation of a ligand in all control tissues where anamount of ligand is detectable.

The terms “targeting ligand”, “targeting molecule”, “homing ligand”, and“homing molecule” as used herein each refer to a ligand that displaystargeting activity. In some embodiments, a targeting ligand displaysselective targeting.

The term “binding” refers to an affinity between two molecules, forexample, a ligand and a target molecule. As used herein, “binding” meansa preferential binding of one molecule for another in a mixture ofmolecules. The binding of a ligand to a target molecule can beconsidered specific if the binding affinity is in some embodiments about1×10⁴ M⁻¹ to about 1×10⁶ M⁻¹ or greater.

The phrase “specifically (or selectively) binds”, when referring to thebinding capacity of a ligand, refers to a binding reaction which isdeterminative of the presence of the protein in a heterogeneouspopulation of proteins and other biological materials. The phrase“specifically binds” also refers to selectively targeting, as definedhereinabove.

The phases “substantially lack binding” or “substantially no binding”,as used herein to describe binding of a ligand in a control tissue,refers to a level of binding that encompasses non-specific or backgroundbinding, but does not include specific binding.

The term “tumor” as used herein refers to both primary and metastasizedsolid tumors and carcinomas of any tissue in a subject, including butnot limited to breast; colon; rectum; lung; oropharynx; hypopharynx;esophagus; stomach; pancreas; liver; gallbladder; bile ducts; smallintestine; urinary tract including kidney, bladder and urothelium;female genital tract including cervix, uterus, ovaries (e.g.,choriocarcinoma and gestational trophoblastic disease); male genitaltract including prostate, seminal vesicles, testes and germ cell tumors;endocrine glands including thyroid, adrenal, and pituitary; skin (e.g.,hemangiomas and melanomas), bone or soft tissues; blood vessels (e.g.,Kaposi's sarcoma); brain, nerves, eyes, and meninges (e.g.,astrocytomas, gliomas, glioblastomas, retinoblastomas, neuromas,neuroblastomas, Schwannomas and meningiomas). The term “tumor” alsoencompasses solid tumors arising from hematopoietic malignancies such asleukemias, including chloromas, plasmacytomas, plaques and tumors ofmycosis fungoides and cutaneous T-cell lymphoma/leukemia, and lymphomasincluding both Hodgkin's and non-Hodgkin's lymphomas.

The term “subject” as used herein refers to any invertebrate orvertebrate species. The methods and compositions disclosed herein areparticularly useful in the treatment and diagnosis of warm-bloodedvertebrates. Thus, the presently disclosed subject matter concernsmammals and birds. More particularly contemplated is the treatmentand/or diagnosis of mammals such as humans, as well as those mammals ofimportance due to being endangered (such as Siberian tigers), ofeconomic importance (animals raised on farms for consumption by humans)and/or social importance (animals kept as pets or in zoos) to humans,for instance, carnivores other than humans (such as cats and dogs),swine (pigs, hogs, and wild boars), ruminants (such as cattle, oxen,sheep, giraffes, deer, goats, bison, and camels), and horses. Alsocontemplated is the treatment of birds, including the treatment of thosekinds of birds that are endangered, kept in zoos, as well as fowl, andmore particularly domesticated fowl, e.g., poultry, such as turkeys,chickens, ducks, geese, guinea fowl, and the like, as they are also ofeconomic importance to humans. Thus, contemplated is the treatment oflivestock, including, but not limited to, domesticated swine (pigs andhogs), ruminants, horses, poultry, and the like.

The term “about”, as used herein when referring to a measurable valuesuch as an amount of weight, time, dose (e.g. radiation dose), etc. ismeant to encompass variations of in some embodiments ±20%, in someembodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, andin some embodiments ±0.1% from the specified amount, as such variationsare appropriate to perform the disclosed method.

II. Guided Drug Delivery Using Ligands

Ionizing radiation induces proteins in tumor vascular endotheliumthrough transcriptional induction and/or posttranslational modificationof cell adhesion molecules such as integrins (Hallahan et al., 1995a;Hallahan et al., 1996; Hallahan et al., 1998; Hallahan & Virudachalam,1999). For example, radiation induces activation of the integrinα_(2b)β₃, also called the fibrinogen receptor, on platelets. The inducedmolecules can serve as binding sites for targeting ligands.

Although several radiation-induced molecules within tumor blood vesselshave been identified and characterized, the α_(2b)β₃ target for drugdelivery achieves the greatest site-specific peptide binding withinirradiated tumor blood vessels. ¹³¹I-labeled fibrinogen bindsspecifically to tumors following exposure to ionizing radiation (U.S.Pat. No. 6,159,443). Peptides within fibrinogen that bind to theradiation-induced α_(2b)β₃ receptor include HHLGGAKQAGDV (SEQ ID NO: 16)and the RGD peptide (Hallahan et al., 2001a).

The presently disclosed subject matter includes a study of the targetingactivity of α_(2b)β₃ ligands in tumor-bearing subjects. Example 1describes guided drug delivery (e.g., radiation guided drug delivery) inanimal models using ligand-conjugated liposomes and microspheres.Clinical trials using a radiolabeled α_(2b)β₃ ligand support thefeasibility of guided drug delivery in humans, as described in Example2. See also Hallahan et al., 2001a.

Despite the successes of guided drug delivery using α_(2b)β₃ ligands inexperimental models, the clinical application of this approach islimited by nonspecific binding of the targeting ligand at sites otherthan the tumor (Hallahan et al., 2001b). In addition, previousobservations of radiation-induced molecules have employed radiationdoses that are sufficient to limit blood flow, as described in Example3. Thus, ligands are sought that demonstrate improved tumor specificityand binding to target molecules induced by reduced radiation doses.

III. Identification of Ligands that Bind Irradiated Tumors

Approaches for optimizing peptide binding affinity and specificity haveincluded modification of peptide conformation and addition of flankingamino acids to extend the minimal binding motif. For example, aminoacids C-terminal to the RGD sequence are differentially conserved inRGD-containing ligands, and this variation correlates with differencesin binding specificity (Cheng et al., 1994; Koivunen et al., 1994).Similarly, cyclization of a prototype RGD peptide to restrict itsconformational flexibility improved interaction of the peptide with thevitronectin receptor, yet nearly abolished interaction with thefibronectin receptor (Pierschbacher & Ruoslahti, 1987).

Despite conservation of binding motifs among ligands that bindirradiated tumors and recognition of factors that can influence ligandbinding, design of peptide sequences for improved targeting activity isyet unpredictable. Approaches for identifying such peptides havetherefore relied on high volume screening methods to select effectivemotifs from peptide libraries (Koivunen et al., 1993; Healy et al.,1995). However, the utility of in vitro-selected peptides isunpredictable in so far as peptide binding properties are notconsistently recapitulated in vivo. To obviate these challenges, thepresently disclosed subject matter provides a method for in vivoselection of targeting ligands, described further hereinbelow.

Using the in vivo selection method disclosed herein, novel targetingligands were identified that can be used for guided drug delivery (e.g.,radiation guided drug delivery). Representative peptide ligands are setforth as SEQ ID NOs: 1-13, 26-69, and 71-86. Representative antibodyligands are set forth as SEQ ID NOs: 18, 20, 22, and 24. The novelligands display improved specificity of binding to irradiated tumors andare effective for targeting using low dose irradiation. The disclosedtargeting ligands also offer benefits including moderate cost ofpreparation and ease of handling.

III.A. Libraries

As used herein, the term “library” means a collection of molecules. Alibrary can contain a few or a large number of different molecules,varying from about ten molecules to several billion molecules or more. Amolecule can comprise a naturally occurring molecule, or a syntheticmolecule (i.e., a molecule that is not found in nature). Optionally, asdescribed further hereinbelow, a plurality of different libraries can beemployed simultaneously for in vivo panning.

Representative libraries include but are not limited to a peptidelibrary (U.S. Pat. Nos. 6,156,511, 6,107,059, 5,922,545, and 5,223,409),an oligomer library (U.S. Pat. Nos. 5,650,489 and 5,858,670), an aptamerlibrary (U.S. Pat. Nos. 6,180,348 and 5,756,291), a small moleculelibrary (U.S. Pat. Nos. 6,168,912 and 5,738,996), a library ofantibodies or antibody fragments (U.S. Pat. Nos. 6,174,708, 6,057,098,5,922,254, 5,840,479, 5,780,225, 5,702,892, and 5,667,988), a library ofnucleic acid-protein fusions (U.S. Pat. No. 6,214,553), and a library ofany other affinity agent that can potentially bind to an irradiatedtumor (e.g., U.S. Pat. Nos. 5,948,635, 5,747,334, and 5,498,538).

The molecules of a library can be produced in vitro, or they can besynthesized in vivo, for example by expression of a molecule in vivo.Also, the molecules of a library can be displayed on any relevantsupport, for example, on bacterial pili (Lu et al., 1995) or on phage(Smith, 1985).

A library can comprise a random collection of molecules. Alternatively,a library can comprise a collection of molecules having a bias for aparticular sequence, structure, or conformation. See e.g., U.S. Pat.Nos. 5,264,563 and 5,824,483. Methods for preparing libraries containingdiverse populations of various types of molecules are known in the art,for example as described in U.S. patents cited hereinabove. Numerouslibraries are also commercially available.

A library useful for in vivo panning as disclosed herein can comprise insome embodiments a library of ten or more diverse molecules, in someembodiments a library of one hundred or more diverse molecules, and insome embodiments a library of one billion or more diverse molecules.Representative diverse molecules include peptides, peptide mimetics,proteins, antibodies or fragments thereof, small molecules, nucleicacids, and combinations thereof. In some embodiments, a library ofpeptides, antibodies, or a combination thereof is used for in vivopanning. A library can further comprise a library of diverse moleculesthat is recovered following in vitro panning.

In some embodiments of the presently disclosed subject matter, a peptidelibrary can be used to perform the disclosed in vivo panning methods. Apeptide library comprises peptides comprising in some embodiments threeor more amino acids, in some embodiments at least five, six, seven, oreight amino acids, in some embodiments up to 50 amino acids or 100 aminoacids, and in some embodiments up to about 200 to 300 amino acids.

The peptides can be linear, branched, or cyclic, and can includenonpeptidyl moieties. The peptides can comprise naturally occurringamino acids, synthetic amino acids, genetically encoded amino acids,non-genetically encoded amino acids, and combinations thereof.

A biased peptide library can also be used, a biased library comprisingpeptides wherein one or more (but not all) residues of the peptides areconstant. For example, an internal residue can be constant, so that thepeptide sequence is represented as:

-   -   (Xaa₁)_(m)-(AA)₁-(Xaa₂)_(n)        where Xaa₁ and Xaa₂ are any amino acid, or any amino acid except        cysteine, wherein Xaa₁ and Xaa₂ are the same or different amino        acids, m and n indicate a number Xaa residues, wherein in some        embodiments m and n are independently chosen from the range of 2        residues to 20 residues, in some embodiments m and n are chosen        from the range of 4 residues to 9 residues, and AA is the same        amino acid for all peptides in the library. In some embodiments,        AA is located at or near the center of the peptide. More        specifically, in some embodiments m and n are not different by        more than 2 residues; in some embodiments m and n are equal.

In some embodiments, AA is tryptophan, proline, or tyrosine. In someembodiments, AA is phenylalanine, histidine, arginine, aspartate,leucine, or isoleucine. In some embodiments, AA is asparagine, serine,alanine, or methionine. In some embodiments, AA is cysteine or glycine.

A biased library used for in vivo panning also includes a librarycomprising molecules previously selected by in vitro panning methods.See Example 8.

In some embodiments of the presently disclosed subject matter, themethod for in vivo panning is performed using a phage peptide library.Phage display is a method to discover peptide ligands while minimizingand optimizing the structure and function of proteins. Phage are used asa scaffold to display recombinant libraries of peptides and provide ameans to recover and amplify the peptides that bind to putative receptormolecules in vivo. In vivo phage selection simultaneously providespositive and subtractive screens based on the spatial separation ofnormal tissues and tumors. Phage that specifically bind the vasculatureof normal tissues are removed while specific phage that bind targetmolecules present in irradiated tumors are enriched through serialrounds of biopanning.

The T7 phage has an icosahedral capsid made of 415 proteins encoded bygene 10 during its lytic phase. The T7 phage display system has thecapacity to display peptides up to 15 amino acids in size at a high copynumber (415 per phage). Unlike filamentous phage display systems,peptides displayed on the surface of 17 phage are not capable of peptidesecretion. T7 phage also replicate more rapidly and are extremely robustwhen compared to other phage. The stability allows for biopanningselection procedures that require persistent phage infectivity.Accordingly, the use of T7-based phage display is an aspect of apreferred embodiment of the presently disclosed subject matter. Example4 describes a representative method for preparation of a 17 phagepeptide library that can be used to perform the in vivo panning methodsdisclosed herein.

A phage peptide library to be used in accordance with the panningmethods of the presently disclosed subject matter can also beconstructed in a filamentous phage, for example M13 or M13-derivedphage. In some embodiments, the encoded antibodies are displayed at theexterior surface of the phage, for example by fusion to M13 vitalprotein 8. Methods for preparing M13 libraries can be found in Sambrook& Russell, 2001, among other places.

In some embodiments, the method for in vivo panning is performed using aphage antibody library, as described in Example 8. Such a library can beconstructed, for example, in M13 or M13-derived phage. See e.g., U.S.Pat. Nos. 6,225,447; 5,580,717; 5,702,892.

III.B. In Vivo Panning for Ligands that Bind Irradiated Tumors

The presently disclosed subject matter provides a method for in vivopanning for ligands that bind irradiated tumors. As used herein, theterm “in vivo panning” refers to a method of screening a library forselection of a ligand that homes to an irradiated tumor.

The term “in vivo”, as used herein to describe methods of panning orligand selection, refers to contacting of one or more ligands toendogenous candidate target molecules, wherein the candidate targetmolecules are naturally present in a subject or a tumor biopsy from asubject, and the contacting occurs in the subject or in the biopsiedtumor. By contrast, “in vitro” panning refers to contacting a library ofcandidate ligands with one or more isolated or recombinantly producedtarget molecules.

Thus, in some embodiments a method for in vivo panning as disclosedherein includes the steps of (a) exposing a tumor to ionizing radiation;(b) administering to a subject a library of diverse molecules; (c)procuring the tumor or fraction thereof; and (d) isolating one or moremolecules of the library of diverse molecules from the tumor, whereby amolecule that binds an irradiated tumor is identified. When performingthe presently disclosed in vivo panning methods, each of the steps ofexposing, administering, procuring, and isolating can be repeated one ormore times to modify and preferably improve ligand selection.

The term “administering to a subject”, when used to describe provisionof a library of molecules, is used in its broadest sense to mean thatthe library is delivered to the irradiated tumor. For example, a librarycan be provided to the circulation of the subject by injection orcannulization such that the molecules can pass through the tumor.

The in vivo panning methods of the presently disclosed subject mattercan further comprise administering the library to isolated tumor cellsor to isolated proteins prior to administering the library to a subjector to a tumor. For example, in vitro panning methods can be performed toselect ligands that bind to particular tumor neoantigens, followed byperformance of the in vivo panning methods as disclosed herein.

Thus, in some embodiments a library can be administered to an isolatedtumor or tumor biopsy. Thus, in some embodiments a method for in vivopanning can also comprise: (a) exposing a tumor and a control tissue toionizing radiation; (b) administering to the tumor and to the controltissue a library of diverse molecules; (c) detecting one or moremolecules of the library that bind to the tumor and that substantiallylack binding to the control tissue, whereby a molecule that binds anirradiated tumor is identified. In some embodiments, the methods canfurther comprise (a) isolating the tumor and the control tissue, and (b)administering the library to the tumor and to the control tissue invitro.

The in vivo panning methods of the presently disclosed subject mattercan further comprise administering the library to isolated tumor cellsor to isolated proteins prior to administering the library to a subjector to a tumor. For example, in vitro panning methods can be performed toselect ligands that bind to particular tumor neoantigens, followed byperformance of the in vivo panning methods as disclosed herein.

In some embodiments of the presently disclosed subject matter, theradiation treatment comprises administration of less than about 2 Gyionizing radiation. In some embodiments, the radiation treatmentcomprises at least about 2 Gy ionizing radiation, in some embodimentsabout 2 Gy to about 3 Gy ionizing radiation, and in some embodimentsabout 2 Gy to about 6 Gy ionizing radiation. In some embodiments,radiation treatment comprises about 10 Gy to about 20 Gy ionizingradiation.

The methods of the presently disclosed subject matter can be performedusing any tumor-bearing subject or any subject suspected of having atumor. In some embodiments, a subject is a warm-blooded vertebrate, insome embodiments a mammal, and in some embodiments a human.

In some embodiments of the presently disclosed subject matter, a libraryis administered to a tumor-bearing human subject following irradiationof the tumor. Methods and appropriate doses for administration of alibrary to a human subject are described in PCT InternationalPublication No. WO 01/09611.

Example 5 describes a representative procedure for in vivo panning ofphage-displayed peptide ligands that bind to irradiated tumor vessels inaccordance with the presently disclosed subject matter. Briefly, peptidebinding was studied in tumor blood vessels of 2 distinct tumor models:(1) GL261 glioma, and (2) Lewis lung carcinoma. Tumors were irradiatedwith 3 Gy to facilitate identification of peptide sequences that bindtumors exposed to a minimal dose of ionizing radiation. Phage wereadministered by tail vein injection into tumor bearing mice followingirradiation. Phage were recovered from the tumor thereafter. Followingmultiple rounds of sequential in vivo binding to irradiated tumors,phage were recovered and individual phage were randomly picked andsequenced. Recovered phage were additionally tested for targetingactivity in an animal model of melanoma, as described in Example 6.

Example 8 describes a representative procedure for in vivo panning ofphage-displayed ligands comprising single chain antibodies. The libraryused for in vivo panning was a biased library in that a pool of antibodyligands that bind to radiation-induced antigens were pre-selected invitro.

III.C. In Vitro Panning for Nuclear Targeting Ligands

Example 12 describes a representative procedure for in vitro panning ofphage-displayed peptide ligands that can be used to target therapeuticand/or diagnostic compositions to the nucleus of tumor cells. After invitro panning, the ability of identified peptides to target tumor cellsin vivo are confirmed using the in vivo panning techniques disclosedherein.

III.D. Recovery of Targeting Ligands

Methods for identifying targeting ligands that bind an irradiated tumorare selected based on one or more characteristics common to themolecules present in the library. For example, mass spectrometry and/orgas chromatography can be used to resolve molecules that home to anirradiated tumor. Thus, where a library comprises diverse moleculesbased generally on the structure of an organic molecule, determining thepresence of a parent peak for the particular molecule can identify aligand that binds a radiation-induced target molecule.

If desired, a molecule can be linked to a tag, which can facilitaterecovery or identification of the molecule. A representative tag is anoligonucleotide or a small molecule such as biotin. See e.g., Brenner &Lerner, 1992 and U.S. Pat. No. 6,068,829. In addition, a tag can be asupport or surface to which a molecule can be attached. For example, asupport can be a biological tag such as a virus or virus-like particlesuch as a bacteriophage (“phage”); a bacterium; or a eukaryotic cellsuch as yeast, an insect cell, or a mammalian cell (e.g., an endothelialprogenitor cell or a leukocyte); or can be a physical tag such as aliposome or a microbead. In some embodiments, a support has a diameterless than about 10 μm to about 50 μm in its shortest dimension, suchthat the support can pass relatively unhindered through the capillarybeds present in the subject and not occlude circulation. In addition, asupport can be nontoxic and biodegradable, particularly where thesubject used for in vivo panning is not sacrificed for isolation oflibrary molecules from the tumor. Where a molecule is linked to asupport, the part of the molecule suspected of being able to interactwith a target in a cell in the subject is preferably positioned so as beable to participate in the interaction.

III.E. Peptide Ligands

A targeting peptide of the presently disclosed subject matter can besubject to various changes, substitutions, insertions, and deletionswhere such changes provide for certain advantages in its use. Thus, theterm “peptide” encompasses any of a variety of forms of peptidederivatives, that include amides, conjugates with proteins, cyclizedpeptides, polymerized peptides, conservatively substituted variants,analogs, fragments, peptoids, chemically modified peptides, and peptidemimetics. The terms “targeting peptide” and “peptide ligand” refer to apeptide as defined hereinabove that binds to an irradiated tumor. Anexemplary peptide ligand of the presently disclosed subject matter canbind to an irradiated tumor of in some embodiments at least one tumortype, in some embodiments two or more tumor types, and in someembodiments three or more tumor types. In some embodiments, a targetingligand can bind to an irradiated glioma, melanoma, and/or a Lewis Lungcarcinoma.

Peptides of the presently disclosed subject matter can comprisenaturally occurring amino acids, synthetic amino acids, geneticallyencoded amino acids, non-genetically encoded amino acids, andcombinations thereof. Peptides can include both L-form and D-form aminoacids.

Representative non-genetically encoded amino acids include but are notlimited to 2-aminoadipic acid; 3-aminoadipic acid; β-aminopropionicacid; 2-aminobutyric acid; 4-aminobutyric acid (piperidinic acid);6-aminocaproic acid; 2-aminoheptanoic acid; 2-aminoisobutyric acid;3-aminoisobutyric acid; 2-aminopimelic acid; 2,4-diaminobutyric acid;desmosine; 2,2′-diaminopimelic acid; 2,3-diaminopropionic acid;N-ethylglycine; N-ethylasparagine; hydroxylysine; allo-hydroxylysine;3-hydroxyproline; 4-hydroxyproline; isodesmosine; allo-isoleucine;N-methylglycine (sarcosine); N-methylisoleucine; N-methylvaline;norvaline; norleucine; and ornithine.

Representative derivatized amino acids include for example, thosemolecules in which free amino groups have been derivatized to form aminehydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups,t-butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Freecarboxyl groups can be derivatized to form salts, methyl and ethylesters or other types of esters or hydrazides. Free hydroxyl groups canbe derivatized to form O-acyl or O-alkyl derivatives. The imidazolenitrogen of histidine can be derivatized to form N-im-benzylhistidine.

The term “conservatively substituted variant” refers to a peptidecomprising an amino acid residue sequence substantially identical to asequence of a reference ligand of radiation-induced target in which oneor more residues have been conservatively substituted with afunctionally similar residue and which displays the targeting activityas described herein. The phrase “conservatively substituted variant”also includes peptides wherein a residue is replaced with a chemicallyderivatized residue, provided that the resulting peptide displaystargeting activity as disclosed herein.

Examples of conservative substitutions include the substitution of onenon-polar (hydrophobic) residue such as isoleucine, valine, leucine ormethionine for another; the substitution of one polar (hydrophilic)residue for another such as between arginine and lysine, betweenglutamine and asparagine, between glycine and serine; the substitutionof one basic residue such as lysine, arginine or histidine for another;or the substitution of one acidic residue, such as aspartic acid orglutamic acid for another.

Peptides of the presently disclosed subject matter also include peptidescomprising one or more additions and/or deletions or residues relativeto the sequence of a peptide whose sequence is disclosed herein, so longas the requisite targeting activity of the peptide is maintained. Theterm “fragment” refers to a peptide comprising an amino acid residuesequence shorter than that of a peptide disclosed herein.

Additional residues can also be added at either terminus of a peptidefor the purpose of providing a “linker” by which the peptides of thepresently disclosed subject matter can be conveniently affixed to alabel or solid matrix, or carrier. Amino acid residue linkers areusually at least one residue and can be 40 or more residues, more often1 to 10 residues, but do alone not constitute radiation-induced targetligands. Typical amino acid residues used for linking are tyrosine,cysteine, lysine, glutamic and aspartic acid, or the like. In addition,a peptide can be modified by terminal-NH₂ acylation (e.g., acetylation,or thioglycolic acid amidation) or by terminal-carboxylamidation (e.g.,with ammonia, methylamine, and the like terminal modifications).Terminal modifications are useful, as is well known, to reducesusceptibility by proteinase digestion, and therefore serve to prolonghalf life of the peptides in solutions, particularly biological fluidswhere proteases can be present.

Peptide cyclization is also a useful terminal modification, and in someembodiments is particularly preferred also because of the stablestructures formed by cyclization and in view of the biologicalactivities observed for such cyclic peptides as described herein. Anexemplary method for cyclizing peptides is described by Schneider &Eberle, 1993. Typically, tertbutoxycarbonyl protected peptide methylester is dissolved in methanol and sodium hydroxide solution are addedand the admixture is reacted at 20° C. to hydrolytically remove themethyl ester protecting group. After evaporating the solvent, thetertbutoxycarbonyl protected peptide is extracted with ethyl acetatefrom acidified aqueous solvent. The tertbutoxycarbonyl protecting groupis then removed under mildly acidic conditions in dioxane cosolvent. Theunprotected linear peptide with free amino and carboxyl termini soobtained is converted to its corresponding cyclic peptide by reacting adilute solution of the linear peptide, in a mixture of dichloromethaneand dimethylformamide, with dicyclohexylcarbodiimide in the presence of1-hydroxybenzotriazole and N-methylmorpholine. The resultant cyclicpeptide is then purified by chromatography.

The term “peptoid” as used herein refers to a peptide wherein one ormore of the peptide bonds are replaced by pseudopeptide bonds includingbut not limited to a carba bond (CH₂—CH₂), a depsi bond (CO—O), ahydroxyethylene bond (CHOH—CH₂), a ketomethylene bond (CO—CH₂), amethylene-oxy bond (CH₂—O), a reduced bond (CH₂—NH), a thiomethylenebond (CH₂—S), a thiopeptide bond (CS—NH), and an N-modified bond(—NRCO—). See e.g. Corringer et al., 1993; Garbay-Jaureguiberry et al.,1992; Tung et al., 1992; Urge et al., 1992; Pavone et al., 1993.

Peptides of the presently disclosed subject matter, including peptoids,can be synthesized by any of the techniques that are known to thoseskilled in the art of peptide synthesis. Synthetic chemistry techniques,such as a solid-phase Merrifield-type synthesis, are preferred forreasons of purity, antigenic specificity, freedom from undesired sideproducts, ease of production and the like. A summary of representativetechniques can be found in Stewart & Young, 1969; Merrifield, 1969;Fields & Noble, 1990; and Bodanszky, 1993. Solid phase synthesistechniques can be found in Andersson et al., 2000, references citedtherein, and in U.S. Pat. Nos. 6,015,561, 6,015,881, 6,031,071, and4,244,946. Peptide synthesis in solution is described by Schröder &Lübke, 1965. Appropriate protective groups usable in such synthesis aredescribed in the above texts and in McOmie, 1973. Peptides that includenaturally occurring amino acids can also be produced using recombinantDNA technology. In addition, peptides comprising a specified amino acidsequence can be purchased from commercial sources (e.g., Biopeptide Co.,LLC of San Diego, Calif., United States of America, and PeptidoGenics ofLivermore, Calif., United States of America).

The term “peptide mimetic” as used herein refers to a ligand that mimicsthe biological activity of a reference peptide, by substantiallyduplicating the targeting activity of the reference peptide, but it isnot a peptide or peptoid. In some embodiments, a peptide mimetic has amolecular weight of less than about 700 daltons.

In some embodiments, a peptide mimetic can be designed by (a)identifying the pharmacophoric groups responsible for the targetingactivity of a peptide; (b) determining the spatial arrangements of thepharmacophoric groups in the active conformation of the peptide; and (c)selecting a pharmaceutically acceptable template upon which to mount thepharmacophoric groups in a manner that allows them to retain theirspatial arrangement in the active conformation of the peptide. Foridentification of pharmacophoric groups responsible for targetingactivity, mutant variants of the peptide can be prepared and assayed fortargeting activity.

Alternatively or in addition, the three-dimensional structure of acomplex of the peptide and its target molecule can be examined forevidence of interactions, for example the fit of a peptide side chaininto a cleft of the target molecule, potential sites for hydrogenbonding, etc. The spatial arrangements of the pharmacophoric groups canbe determined by NMR spectroscopy or X-ray diffraction studies. Aninitial three-dimensional model can be refined by energy minimizationand molecular dynamics simulation. A template for modeling can beselected by reference to a template database and will typically allowthe mounting of 2-8 pharmacophores. A peptide mimetic is identifiedwherein addition of the pharmacophoric groups to the template maintainstheir spatial arrangement as in the peptide.

A peptide mimetic can also be identified by assigning a hashed bitmapstructural fingerprint to the peptide based on its chemical structure,and determining the similarity of that fingerprint to that of eachcompound in a broad chemical database. The fingerprints can bedetermined using fingerprinting software commercially distributed forthat purpose by Daylight Chemical Information Systems, Inc. (MissionViejo, Calif., United States of America) according to the vendor'sinstructions. Representative databases include but are not limited toSPREI'95 (InfoChem GmbH of MUnchen, Germany), Index Chemicus (ISI ofPhiladelphia, Pa., United States of America), World Drug Index (Derwentof London, United Kingdom), TSCA93 (United States EnvrionmentalProtection Agency), MedChem (Biobyte of Claremont, Calif., United Statesof America), Maybridge Organic Chemical Catalog (Maybridge of Cornwall,United Kingdom), Available Chemicals Directory (MDL Information Systemsof San Leandro, Calif., United States of America), NCI96 (United StatesNational Cancer Institute), Asinex Catalog of Organic Compounds (AsinexLtd. of Moscow, Russia), and NP (InterBioScreen Ltd. of Moscow, Russia).A peptide mimetic of a reference peptide is selected as comprising afingerprint with a similarity (Tanamoto coefficient) of at least 0.85relative to the fingerprint of the reference peptide. Such peptidemimetics can be tested for bonding to an irradiated tumor using themethods disclosed herein.

Additional techniques for the design and preparation of peptide mimeticscan be found in U.S. Pat. Nos. 5,811,392; 5,811,512; 5,578,629;5,817,879; 5,817,757; and 5,811,515.

Any peptide or peptide mimetic of the presently disclosed subject mattercan be used in the form of a pharmaceutically acceptable salt. Suitableacids which are capable of the peptides with the peptides of thepresently disclosed subject matter include inorganic acids such astrifluoroacetic acid (TFA), hydrochloric acid (HCl), hydrobromic acid,perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, phosphoricacetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid,oxalic acid, malonic acid, succinic acid, maleic acid, fumaric acid,anthranilic acid, cinnamic acid, naphthalene sulfonic acid, sulfanilicacid or the like. HCl and TFA salts are particularly preferred.

Suitable bases capable of forming salts with the peptides of thepresently disclosed subject matter include inorganic bases such assodium hydroxide, ammonium hydroxide, potassium hydroxide and the like;and organic bases such as mono-di- and tri-alkyl and aryl amines (e.g.triethylamine, diisopropyl amine, methyl amine, dimethyl amine and thelike), and optionally substituted ethanolamines (e.g. ethanolamine,diethanolamine and the like).

III.F. Antibody Ligands

A targeting antibody of the presently disclosed subject matter comprisesan antibody identified by the in vivo panning methods disclosed herein.In some embodiments, an antibody targeting ligand comprises (a) apolypeptide comprising an amino acid sequence of SEQ ID NO: 18, 20, 22,or 24; (b) a polypeptide substantially identical to SEQ ID NO: 18, 20,22, or 24; (c) a polypeptide encoded by SEQ ID NO: 17, 19, 21, or 23; or(d) a polypeptide substantially identical to SEQ ID NO: 17, 19, 21, or23. Thus, the presently disclosed subject matter also provides in someembodiments an isolated nucleic acid that encodes an antibody targetingligand comprising (a) a nucleic acid molecule comprising the nucleotidesequence of SEQ ID NO: 17, 19, 21, or 23; or (b) a nucleic acid moleculesubstantially identical to SEQ ID NO: 17, 19, 21, or 23.

When phage-displayed antibodies bind to an antigen, they can beaffinity-purified using the antigen. These affinity-purified phage canthen be used to infect and introduce the antibody gene back into E.coli. The E. coli can then be grown and induced to express a soluble,non-phage-displayed, antigen-specific recombinant antibody. Phagedisplay technology is especially useful for producing antibodies toantigens that are either poorly immunogenic or readily degraded and forwhich monoclonal and/or polyclonal antibodies are difficult to obtain.P-selectin, like α_(2b)β₃, is a high priority radiation-inducedneoantigen because it is not accessible to antibodies orimmunoconjugates until after irradiation of tumor vasculature. PhagescFv antibodies have been developed to these proteins by use ofphage-displayed antibody library containing 2×10⁹ members. Negativeselection of phage can be first performed on a control tissue, forexample untreated vascular endothelium. This can eliminate antibodiesthat nonspecifically bind to, for example, unirradiated endothelialcells. Unbound phage can then be recovered and incubated with purifiedradiation-induced neoantigen, for example, P-selectin or α_(2b)β₃integrin. High affinity phage can then be recovered, for example by useof washing at pH 1.

The term “isolated”, as used in the context of a nucleic acid orpolypeptide, indicates that the nucleic acid or polypeptide exists apartfrom its native environment and is not a product of nature. An isolatednucleic acid or polypeptide can exist in a purified form or can exist ina non-native environment such as a transgenic host cell. In oneembodiment of the presently disclosed subject matter, “isolated” refersto the purification of an scFv antibody from a target tissue to which ithas bound.

Nucleic Acids Encoding Targeting Antibodies. The terms “nucleic acidmolecule” or “nucleic acid” each refer to deoxyribonucleotides orribonucleotides and polymers thereof in single-stranded ordouble-stranded. Unless specifically limited, the term encompassesnucleic acids containing known analogues of natural nucleotides thathave similar properties as the reference natural nucleic acid. The terms“nucleic acid molecule” or “nucleic acid” can also be used in place of“gene”, “cDNA”, or “mRNA”. Nucleic acids can be synthesized, or can bederived from any biological source, including any organism.

The term “substantially identical”, as used herein to describe a degreeof similarity between nucleotide sequences, refers to two or moresequences that have in some embodiments at least about least 60%, insome embodiments at least about least 65%, in some embodiments at leastabout 70%, in some embodiments at least about least 75%, in someembodiments at least about 80%, in some embodiments at least about least85%, in some embodiments at least about least 90%, in some embodimentsat least about least 93%, in some embodiments at least about least 95%,in some embodiments at least about least 97%, and in some embodimentsabout 99% nucleotide identity, as measured using one of the followingsequence comparison algorithms (described hereinbelow) or by visualinspection. The substantial identity exists in nucleotide sequences ofin some embodiments at least about 100 residues, in some embodiments atleast about 150 residues, and in some embodiments in nucleotidesequences, comprising a full length coding sequence.

Thus, substantially identical sequences can comprise) mutagenizedsequences, including sequences comprising silent mutations, or variablysynthesized sequences. A mutation or variant sequence can comprise asingle base change.

Another indication that two nucleotide sequences are substantiallyidentical is that the two molecules specifically or substantiallyhybridize to each other under stringent conditions. In the context ofnucleic acid hybridization, two nucleic acid sequences being comparedcan be designated a “probe” and a “target”. A “probe” is a referencenucleic acid molecule, and a “target” is a test nucleic acid molecule,often found within a heterogeneous population of nucleic acid molecules.A “target sequence” is synonymous with a “test sequence”.

An exemplary nucleotide sequence that can be employed for hybridizationstudies or assays includes probe sequences that are complementary to ormimic at least an about 14 to 40 nucleotide sequence of a nucleic acidmolecule of the presently disclosed subject matter. For this purpose, aprobe comprises a region of the nucleic acid molecule other than asequence encoding a common immunoglobulin region. Thus, a probecomprises in some embodiments a sequence encoding a domain of theantibody that comprises an antigen-binding site. In some embodiments,probes comprise 14 to 20 nucleotides, or even longer where desired, suchas 30, 40, 50, 60, 100, 200, 300 nucleotides or up to the full length ofa region of SEQ ID NO: 17, 19, 21, or 23 that encodes an antigen bindingsite. Such fragments can be readily prepared by, for example, chemicalsynthesis of the fragment, by application of nucleic acid amplificationtechnology, or by introducing selected sequences into recombinantvectors for recombinant production.

The phrase “hybridizing specifically to” refers to the binding,duplexing, or hybridizing of a molecule only to a particular nucleotidesequence under stringent conditions when that sequence is present in acomplex nucleic acid mixture (e.g., total cellular DNA or RNA).

The phrase “hybridizing substantially to” refers to complementaryhybridization between a probe nucleic acid molecule and a target nucleicacid molecule and embraces minor mismatches that can be accommodated byreducing the stringency of the hybridization media to achieve thedesired hybridization.

“Stringent hybridization conditions” and “stringent hybridization washconditions” in the context of nucleic acid hybridization experimentssuch as Southern and Northern blot analysis are both sequence- andenvironment-dependent. Longer sequences hybridize specifically at highertemperatures. An extensive guide to the hybridization of nucleic acidsis found in Tijssen, 1993. Generally, highly stringent hybridization andwash conditions are selected to be about 5° C. lower than the thermalmelting point (T_(m)) for the specific sequence at a defined ionicstrength and pH. Typically, under “stringent conditions” a probe willhybridize specifically to its target subsequence, but to no othersequences.

The T_(m) is the temperature (under defined ionic strength and pH) atwhich 50% of the target sequence hybridizes to a perfectly matchedprobe. Very stringent conditions are selected to be equal to the T_(m)for a particular probe. An example of stringent hybridization conditionsfor Southern or Northern Blot analysis of complementary nucleic acidshaving more than about 100 complementary residues is overnighthybridization in 50% formamide with 1 mg of heparin at 42° C. An exampleof highly stringent wash conditions is 15 minutes in 0.1×SSC at 65° C.An example of stringent wash conditions is 15 minutes in 0.2×SSC bufferat 65° C. See Sambrook & Russell, 2001 for a description of SSC buffer.

Often, a high stringency wash is preceded by a low stringency wash toremove background probe signal. An example of medium stringency washconditions for a duplex of more than about 100 nucleotides, is 15minutes in 1×SSC at 45° C. An example of low stringency wash for aduplex of more than about 100 nucleotides, is 15 minutes in 4× to 6×SSCat 40° C. For short probes (e.g., about 10 to 50 nucleotides), stringentconditions typically involve salt concentrations of less than about 1MNa⁺ ion, typically about 0.01 to 1M Na⁺ ion concentration (or othersalts) at pH 7.0-8.3, and the temperature is typically at least about30° C. Stringent conditions can also be achieved with the addition ofdestabilizing agents such as formamide. In general, a signal to noiseratio of 2-fold (or higher) than that observed for an unrelated probe inthe particular hybridization assay indicates detection of a specifichybridization.

The following are examples of hybridization and wash conditions that canbe used to identify nucleotide sequences that are substantiallyidentical to reference nucleotide sequences of the presently disclosedsubject matter: in some embodiments a probe nucleotide sequencehybridizes to a target nucleotide sequence in 7% sodium dodecyl sulfate(SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. followed by washing in 2×SSC,0.1% SDS at 50° C.; in some embodiments a probe and target sequencehybridize in 7% sodium dodecyl sulfate (SOS), 0.5 M NaPO₄, 1 mM EDTA at50° C. followed by washing in 1×SSC, 0.1% SDS at 50° C.; in someembodiments a probe and target sequence hybridize in 7% sodium dodecylsulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. followed by washing in0.5×SSC, 0.1% SDS at 50° C.; in some embodiments a probe and targetsequence hybridize in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mMEDTA at 50° C. followed by washing in 0.1×SSC, 0.1% SDS at 50° C.; andin some embodiments a probe and target sequence hybridize in 7% sodiumdodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. followed bywashing in 0.1×SSC, 0.1% SDS at 65° C.

A further indication that two nucleic acid sequences are substantiallyidentical is that proteins encoded by the nucleic acids aresubstantially identical, share an overall three-dimensional structure,or are biologically functional equivalents. These terms are definedfurther hereinbelow. Nucleic acid molecules that do not hybridize toeach other under stringent conditions are still substantially identicalif the corresponding proteins are substantially identical. This canoccur, for example, when two nucleotide sequences are significantlydegenerate as permitted by the genetic code.

The term “conservatively substituted variants” refers to nucleic acidsequences having degenerate codon substitutions wherein the thirdposition of one or more selected (or all) codons is substituted withmixed-base and/or deoxyinosine residues. See Batzer et al., 1991;Ohtsuka et al., 1985; Rossolini et al., 1994.

The term “subsequence” refers to a sequence of nucleic acids thatcomprises a part of a longer nucleic acid sequence. An exemplarysubsequence is a probe, described hereinabove, or a primer. The term“primer” as used herein refers to a contiguous sequence comprising insome embodiments about 8 or more deoxyribonucleotides orribonucleotides, in some embodiments about 10-20 nucleotides, and insome embodiments about 20-30 nucleotides of a selected nucleic acidmolecule. The primers of the presently disclosed subject matterencompass oligonucleotides of sufficient length and appropriate sequenceso as to provide initiation of polymerization on a nucleic acid moleculeof the presently disclosed subject matter.

The term “elongated sequence” refers to an addition of nucleotides (orother analogous molecules) incorporated into the nucleic acid. Forexample, a polymerase (e.g., a DNA polymerase) can add sequences at the3′ terminus of the nucleic acid molecule. In addition, the nucleotidesequence can be combined with other DNA sequences, such as promoters,promoter regions, enhancers, polyadenylation signals, intronicsequences, additional restriction enzyme sites, multiple cloning sites,and other coding segments.

Nucleic acids of the presently disclosed subject matter can be cloned,synthesized, recombinantly altered, mutagenized, or combinationsthereof. Standard recombinant DNA and molecular cloning techniques usedto isolate nucleic acids are known in the art. Site-specific mutagenesisto create base pair changes, deletions, or small insertions are alsoknown in the art. See e.g., Sambrook & Russell, 2001; Silhavy et al.,1984; Glover & Hames, 1995; Ausubel, 1995.

Single Chain Antibody Polypeptides. The term “substantially identical”,as used herein to describe a level of similarity between a polypeptidecomprising an antibody targeting ligand and a polypeptide to SCN1A,refers to a sequence having in some embodiments at least about 45%, insome embodiments at least about 50%, in some embodiments at least about60%, in some embodiments at least about 70%, in some embodiments atleast about 80%, in some embodiments at least about 90%, in someembodiments at least about 95%, and in some embodiments at least about99% sequence identity to SEQ ID NO: 17, 19, 21, or 23, when comparedover the full length of the single chain polypeptide. The term “fulllength”, as used herein to describe an antibody targeting ligand,comprises an amino acid sequence having 254 amino acids. Methods fordetermining percent identity are defined hereinbelow.

Substantially identical polypeptides also encompass two or morepolypeptides sharing a conserved three-dimensional structure.Computational methods can be used to compare structural representations,and structural models can be generated and easily tuned to identifysimilarities around important active sites or ligand binding sites. SeeSaqi et al., 1999; Barton, 1998; Henikoff et al., 2000; Huang et al.,2000.

Substantially identical proteins also include proteins comprising anamino acid sequence comprising amino acids that are functionallyequivalent to amino acids of SEQ ID NOs: 18, 20, 22, and 24. The term“functionally equivalent” in the context of amino acid sequences isknown in the art and is based on the relative similarity of the aminoacid side-chain substituents. See Henikoff & Henikoff, 2000. Relevantfactors for consideration include side-chain hydrophobicity,hydrophilicity, charge, and size. For example, arginine, lysine, andhistidine are all positively charged residues; that alanine, glycine,and serine are all of similar size; and that phenylalanine, tryptophan,and tyrosine all have a generally similar shape. By this analysis,described further hereinbelow, arginine, lysine, and histidine; alanine,glycine, and serine; and phenylalanine, tryptophan, and tyrosine; aredefined herein as biologically functional equivalents.

In making biologically functional equivalent amino acid substitutions,the hydropathic index of amino acids can be considered. Each amino acidhas been assigned a hydropathic index on the basis of theirhydrophobicity and charge characteristics, these are: isoleucine (+4.5);valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine (+2.5);methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7);serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6);histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5);asparagine (−3.5); lysine (−3.9); and arginine (−4.5).

The importance of the hydropathic amino acid index in conferringinteractive biological function on a protein is generally understood inthe art (Kyte et al., 1982). It is known that certain amino acids can besubstituted for other amino acids having a similar hydropathic index orscore and still retain a similar biological activity. In making changesbased upon the hydropathic index, amino acids can be substituted whosehydropathic indices are in some embodiments within ±2 of the originalvalue, in some embodiments within ±1 of the original value, and in someembodiments within ±0.5 of the original value.

It is also understood in the art that the substitution of like aminoacids can be made effectively on the basis of hydrophilicity. U.S. Pat.No. 4,554,101 describes that the greatest local average hydrophilicityof a protein, as governed by the hydrophilicity of its adjacent aminoacids, correlates with its immunogenicity and antigenicity, e.g., with abiological property of the protein. It is understood that an amino acidcan be substituted for another having a similar hydrophilicity value andstill obtain a biologically equivalent protein.

As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicityvalues have been assigned to amino acid residues: arginine (+3.0);lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3);asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4);proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0);methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8);tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4).

In making changes based upon similar hydrophilicity values, amino acidscan be substituted whose hydrophilicity values are in some embodimentswithin ±2 of the original value, in some embodiments within ±1 of theoriginal value, and in some embodiments within ±0.5 of the originalvalue.

The term “substantially identical” also encompasses polypeptides thatare biologically functional equivalents. The term “functional”, as usedherein to describe polypeptides comprising antibody targeting ligands,refers two or more antibodies that are immunoreactive with a sameradiation-induced target molecule. In some embodiments, the two or moreantibodies specifically bind a same target molecule and substantiallylack binding to a control antigen.

The term “specifically binds”, when used to describe binding of anantibody to a target molecule, refers to binding to a target molecule ina heterogeneous mixture of other polypeptides.

The phases “substantially lack binding” or “substantially no binding”,as used herein to describe binding of an antibody to a controlpolypeptide or sample, refers to a level of binding that encompassesnon-specific or background binding, but does not include specificbinding.

Techniques for detecting antibody-target molecule complexes are known inthe art and include but are not limited to centrifugation, affinitychromatography and other immunochemical methods. In some embodiments, anantibody-target molecule complex can be detected followingadministration of an antibody to a subject as described in Examples 6and 7. In some embodiments, an antibody-target molecule complex can bedetected in vivo by performing radiation-guided drug delivery, whereinthe drug comprises a targeting antibody of SEQ ID NO: 18, 20, 22, or 24and a detectable label, as described in Examples 1 and 2. See also,Manson, 1992; Ishikawa, 1999; Law, 1996.

The presently disclosed subject matter also provides functionalfragments of an antibody targeting polypeptide. Such functional portionneed not comprise all or substantially all of the amino acid sequence ofSEQ ID NO: 18, 20, 22, or 24.

The presently disclosed subject matter also includes functionalpolypeptide sequences that are longer sequences than that of SEQ ID NO:18, 20, 22, or 24. For example, one or more amino acids can be added tothe N-terminus or C-terminus of a antibody targeting ligand. Methods ofpreparing such proteins are known in the art.

Isolated polypeptides and recombinantly produced polypeptides can bepurified and characterized using a variety of standard techniques thatare known to the skilled artisan. See e.g., Schröder & Lübke, 1965;Schneider & Eberle, 1993; Bodanszky, 1993; Ausubel, 1995.

Nucleotide and Amino Acid Sequence Comparisons. The terms “identical” orpercent “identity” in the context of two or more nucleotide orpolypeptide sequences, refer to two or more sequences or subsequencesthat are the same or have a specified percentage of amino acid residuesor nucleotides that are the same, when compared and aligned for maximumcorrespondence, as measured using one of the sequence comparisonalgorithms disclosed herein or by visual inspection.

The term “substantially identical” in regards to a nucleotide orpolypeptide sequence means that a particular sequence varies from thesequence of a naturally occurring sequence by one or more deletions,substitutions, or additions, the net effect of which is to retainbiological activity of a gene, gene product, or sequence of interest.

For sequence comparison, typically one sequence acts as a referencesequence to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer program, subsequence coordinates are designated if necessary,and sequence algorithm program parameters are selected. The sequencecomparison algorithm then calculates the percent sequence identity forthe designated test sequence(s) relative to the reference sequence,based on the selected program parameters.

Optimal alignment of sequences for comparison can be conducted, forexample, by the local homology algorithm of Smith & Waterman, 1981, bythe homology alignment algorithm of Needleman & Wunsch, 1970, by thesearch for similarity method of Pearson & Lipman, 1988, by computerizedimplementations of these algorithms (e.g., programs available in theDISCOVERY STUDIO® package from Accelrys, Inc., San Diego, Calif., UnitedStates of America), or by visual inspection. See generally, Ausubel,1995.

An exemplary algorithm for determining percent sequence identity andsequence similarity is the BLAST algorithm, which is described inAltschul et al., 1990. Software for performing BLAST analyses ispublicly available through the website of the National Center forBiotechnology Information. This algorithm involves first identifyinghigh scoring sequence pairs (HSPs) by identifying short words of lengthW in the query sequence, which either match or satisfy somepositive-valued threshold score T when aligned with a word of the samelength in a database sequence. T is referred to as the neighborhood wordscore threshold. These initial neighborhood word hits act as seeds forinitiating searches to find longer HSPs containing them. The word hitsare then extended in both directions along each sequence for as far asthe cumulative alignment score can be increased. Cumulative scores arecalculated using, for nucleotide sequences, the parameters M (rewardscore for a pair of matching residues; always >0) and N (penalty scorefor mismatching residues; always <0). For amino acid sequences, ascoring matrix is used to calculate the cumulative score. Extension ofthe word hits in each direction are halted when the cumulative alignmentscore falls off by the quantity X from its maximum achieved value, thecumulative score goes to zero or below due to the accumulation of one ormore negative-scoring residue alignments, or the end of either sequenceis reached. The BLAST algorithm parameters W, T, and X determine thesensitivity and speed of the alignment. The BLASTN program (fornucleotide sequences) uses as defaults a wordlength W=11, an expectationE=10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. Foramino acid sequences, the BLASTP program uses as defaults a wordlength(W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix. SeeHenikoff & Henikoff, 1992.

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences. See e.g., Karlin & Altschul, 1993. One measure ofsimilarity provided by the BLAST algorithm is the smallest sumprobability (P(N)), which provides an indication of the probability bywhich a match between two nucleotide or amino acid sequences would occurby chance. For example, a test nucleic acid sequence is consideredsimilar to a reference sequence if the smallest sum probability in acomparison of the test nucleic acid sequence to the reference nucleicacid sequence is in some embodiments less than about 0.1, in someembodiments less than about 0.01, and in some embodiments less thanabout 0.001.

IV. Tumor Diagnosis, Treatment, and Imaging

The presently disclosed subject matter further provides in someembodiments methods and compositions for guided drug delivery (e.g.,radiation guided drug delivery) to a tumor in a subject. The term “drug”as used herein refers to any substance having biological or detectableactivity. Thus, the term “drug” includes a pharmaceutical agent, adiagnostic agent, or a combination thereof. The term “drug” alsoincludes any substance that is desirably delivered to a tumor.

Immunoconjugates compositions of the presently disclosed subject mattercan be monovalent (i.e. they comprise an antibody that binds to only oneepitope present on a radiation-induced neoantigen) or polyvalent. Asused herein, a “polyvalent immunoconjugate composition” refers to animmunoconjugate composition that comprises at least two differentligands (for example, scFv antibodies that bind to radiation-inducedneoantigens) that bind to at least two different targets, at least oneof which is a radiation-induced neoantigen. Thus, in one embodiment apolyvalent immunoconjugate composition comprises a plurality of singlechain fragment variable (scFv) antibodies, human Fab antibodies, orcombinations thereof, wherein the plurality of antibodies or antibodyfragments bind to a plurality of different epitopes, and wherein atleast one of the epitopes is present on a radiation-induced neoantigen.In one embodiment, at least one of the plurality of different epitopesis present on a vascular endothelial cell.

An exemplary polyvalent immunoconjugate is depicted in FIG. 1. As shownin FIG. 1, Antibody 1 binds to an epitope present on endothelium (forexample, tumor endothelium), and Antibody 2 binds to an antigen presenton vascular endothelium. One or both of the epitopes to which Antibody 1and Antibody 2 bind can be radiation-induced neoantigens. This Figuredepicts the epitopes to which Antibodies 1 and 2 bind as beingdifferent, thus the immunoconjugate is a polyvalent immunoconjugate.

However, if Antibody 1 and Antibody 2 bind to the same epitope presenton a radiation-induced neoantigen, the immunoconjugate would bemonovalent.

In accordance with the presently disclosed subject matter,immunoconjugate compositions can be used to deliver therapeutic agentsto target tissues. Such therapeutic agents include, but are not limitedto viruses, radionuclides, cytotoxins, therapeutic genes, andchemotherapeutic agents.

Also in accordance with the presently disclosed subject matter, animmunoconjugate composition, the immunoconjugate composition can furthercomprise a detectable label. In one embodiment, the detectable label isdetectable in vivo. In this embodiment, the detectable label comprises alabel that can be detected using magnetic resonance imaging,scintigraphic imaging, ultrasound, or fluorescence. An exemplarydetectable label that can be used for detection.

Thus, in some embodiments, a composition is prepared, the compositioncomprising a targeting ligand as disclosed herein and a diagnosticagent. In some embodiments, the composition can be used for thedetection of a tumor in a subject by (a) exposing a suspected tumor toionizing radiation; (b) administering to the subject a targeting ligandof the presently disclosed subject matter, wherein the ligand comprisesa detectable label; and (c) detecting the detectable label, whereby atumor is diagnosed. In some embodiments, a method for detecting a tumorcan comprise (a) exposing a suspected tumor to ionizing radiation; (b)biopsing a suspected tumor; (c) contacting a targeting ligand of thepresently disclosed subject matter with the suspected tumor in vitro,wherein the ligand comprises a detectable label; and (d) detecting thedetectable label, whereby a tumor is diagnosed.

A therapeutic composition of the presently disclosed subject matter cancomprise one or more targeting ligands and a therapeutic agent, suchthat the therapeutic agent can be selectively targeted to an irradiatedtumor. Representative therapeutic agents include a radionuclide, acytotoxin, a therapeutic gene, and a chemotherapeutic agent. The one ormore targeting ligands can comprise ligands having diverse molecularfeatures. For example, one or more targeting ligands can comprise bothpeptide and antibody targeting ligands.

In some embodiments, a therapeutic composition can additionally comprisea detectable label, in some embodiments a label that can be detected invivo. The biodistribution of the therapeutic composition so prepared canbe monitored following administration to a subject.

Methods for preparation, labeling, and guided drug delivery usingtargeting ligands of the presently disclosed subject matter aredescribed further hereinbelow. See also Examples 1 and 2.

IV.A. Therapeutic Agents

The novel targeting ligands disclosed here are used to target atherapeutic agent to an irradiated tumor. Representative therapeuticagents include but are not limited to a nucleic acid (e.g., atherapeutic gene) and a small molecule. In some embodiments of thepresently disclosed subject matter, an inactive drug is administered,which is subsequently activated by irradiation (Hallahan et al., 1995b).For example, therapeutic gene expression can be regulated by aradiation-induced promoter (Hallahan et al., 1995b).

Therapeutic Genes. Angiogenesis and suppressed immune response play acentral role in the pathogenesis of malignant disease and tumor growth,invasion, and metastasis. Thus, in some embodiments, a therapeutic geneencodes a polypeptide having an ability to induce an immune responseand/or an anti-angiogenic response in vivo.

The term “immune response” is meant to refer to any response to anantigen or antigenic determinant by the immune system of a vertebratesubject. Exemplary immune responses include humoral immune responses(e.g. production of antigen-specific antibodies) and cell-mediatedimmune responses (e.g. lymphocyte proliferation).

Representative therapeutic proteins with immunostimulatory effectsinclude but are not limited to cytokines (e.g., IL-2, IL-7, IL-12,interferons, granulocyte-macrophage colony-stimulating factor (GM-CSF),tumor necrosis factor alpha (TNF-α)), immunomodulatory cell surfaceproteins (e.g., human leukocyte antigen (HLA proteins), co-stimulatorymolecules, and tumor-associated antigens. See Kirk & Mule, 2000;Mackensen et al., 1997; Walther & Stein, 1999; and references citedtherein.

The term “angiogenesis” refers to the process, by which new bloodvessels are formed. The term “anti-angiogenic response” and“anti-angiogenic activity” as used herein, each refer to a biologicalprocess wherein the formation of new blood vessels is inhibited.

Representative proteins with anti-angiogenic activities that can be usedin accordance with the presently disclosed subject matter include:thrombospondin I (Kosfeld & Frazier, 1993; Tolsma et al., 1993; Dameronet al., 1994), metallospondin proteins (Carpizo & Iruela-Arispe, 2000),class I interferons (Albini et al., 2000), IL12 (Voest et al., 1995),protamine (Ingber et al., 1990), angiostatin (O'Reilly et al., 1994),laminin (Sakamoto et al., 1991), endostatin (O'Reilly et al., 1997), anda prolactin fragment (Clapp et al., 1993). In addition, severalanti-angiogenic peptides have been isolated from these proteins (Maioneet al., 1990; Eijan et al., 1991; Woltering et al., 1991).

A gene therapy construct used in accordance with the methods of thepresently disclosed subject matter can also encode a therapeutic genethat displays both immunostimulatory and anti-angiogenic activities, forexample, IL-12 (see Dias et al., 1998; and references citedhereinbelow), interferon-a (O'Byrne et al., 2000), and references citedtherein), or a chemokine (Nomura & Hasegawa, 2000, and references citedtherein). In addition, a gene therapy construct can encode a geneproduct with immunostimulatory activity and a gene product havinganti-angiogenic activity. See e.g. Narvaiza et al., 2000.

Additional compositions useful for cancer therapy include but are notlimited to genes encoding tumor suppressor gene products/antigens,apoptosis-inducing polypeptides, antimetabolites, suicide gene products,and combinations thereof. See Kirk & Mule, 2000; Mackensen et al., 1997;Walther & Stein, 1999; and references cited therein.

Therapeutic Compounds. In accordance with the methods of the presentlydisclosed subject matter, a therapeutic agent can also comprise acytotoxic agent, a chemotherapeutic agent, a radionuclide, or any otheranti-tumor molecule. Studies using ligand/drug conjugates havedemonstrated that a chemotherapeutic agent can be linked to a ligand toproduce a conjugate that maintains the binding specificity of the ligandand the therapeutic function of the agent. For example, doxorubicin hasbeen linked to antibodies or peptides and the ligand/doxorubicinconjugates display cytotoxic activity (Shih et al., 1994; Lau et al.,1995; Sivam et al., 1995), PCT International Publication No. WO98/10795). Similarly, other anthracyclines, including idarubicin anddaunorubocin, have been chemically conjugated to antibodies, which havefacilitated delivery of effective doses of the agents to tumors(Aboud-Pirak et al., 1989; Rowland et al., 1993). Other chemotherapeuticagents include cis-platinum (Schechter et al., 1991), methotrexate(Shawler et al., 1988; Fitzpatrick & Garnett; 1995) and mitomycin-C(Dillman et al., 1989).

In some embodiments of the presently disclosed subject matter, atherapeutic agent comprises a radionuclide. Radionuclides can beeffectively conjugated to antibodies (Hartmann et al., 1994; Buchsbaumat al., 1995), small molecule ligands (Wilbur, 1992; Fjalling et al.,1996), and peptides (Boerman et al., 2000; Krenning & de Jong, 2000;Kwekkeboom et al., 2000; Virgolini et al., 2001, and references citedtherein), such that administration of the conjugated radionuclidepromotes tumor regression. Representative therapeutic radionuclides andmethods for preparing a radionuclide-labeled agent are described furtherhereinbelow under the heading Scinitaraohic Imaging. For therapeuticmethods of the presently disclosed subject matter, a preferredradionuclide comprises ¹³¹I.

Additional anti-tumor agents that can be conjugated to the targetingligands disclosed herein and used in accordance with the therapeuticmethods of the presently disclosed subject matter include but are notlimited to alkylating agents such as melphalan and chlorambucil (Smythet al., 1987; Aboud-Pirak et al., 1989; Rowland at al., 1993), vincaalkaloids such as vindesine and vinblastine (Aboud-Pirak at al., 1989;Starling et al., 1992), antimetabolites such as 5-fluorouracil,5-fluorouridine and derivatives thereof (Krauer at al., 1992; Henn etal., 1993).

Nuclear Targeting. In some embodiments, the therapeutic and/ordiagnostic compositions of disclosed herein are targeted to the nucleusof a cell (e.g., the nucleus of a tumor cell). Targeting to the cellnucleus can be accomplished using targeting peptides comprising, in someembodiments, any of SEQ ID NOs: 61-69. In some embodiments, thetargeting is to the nucleus of a tumor cell. Targeting to the nucleus ofa tumor cell can be accomplished using a targeting ligand thatcomprises, in some embodiments, a peptide comprising any of SEQ ID NOs:61-69. Targeting to the nucleus of a tumor cell can be accomplishedusing a targeting ligand that comprises, in some embodiments, a peptidecomprising any of SEQ ID NOs: 61-69 in addition to a tumor-targetingpeptide as disclosed herein (e.g., SEQ ID NOs: 1-13, 26-60, and 71-86).

The therapeutic and/or diagnostic compositions that are targeted to thenucleus can comprise any of the therapeutic and/or diagnostic entitiesdisclosed herein, including therapeutic agents and diagnostic agentsdisclosed herein. In some embodiments the nuclear targeting compositioncan be used to deliver additional therapeutic and diagnostic agents thatare therapeutically effective when delivered to the nucleus. Such agentsinclude, but are not limited to polypeptides associated with apoptosisinduction, as well as the nucleotide sequences encoding suchpolypeptides. Exemplary apoptosis-inducing genes and gene productsinclude, but are not limited to bax, bak, and DP5.

IV.B. Preparation of a Therapeutic and/or Diagnostic Composition

The presently disclosed subject matter also provides a method forpreparing a composition for guided drug delivery (e.g., radiation guideddrug delivery). In some embodiments, the method comprises (a) performingin vivo panning, whereby a ligand that binds a radiation-induced tumormolecule is identified; and (b) conjugating the ligand to a drug,whereby a composition for guided drug delivery is prepared. A drug canfurther comprise a drug carrier and can be formulated in any mannersuitable for administration to a subject. In some embodiments, themethod employs a targeting ligand comprising any one of SEQ ID NOs:1-13, 18, 20, 22, 24-69, and 71-86.

Drug Carriers. The compositions of the presently disclosed subjectmatter can further comprise a drug carrier to facilitate drugpreparation and administration. Any suitable drug delivery vehicle orcarrier can be used, including but not limited to a gene therapy vector(e.g., a viral vector or a plasmid), a microcapsule, for example amicrosphere or a nanosphere (Manome et al., 1994; Hallahan, 2001a;Saltzman & Fung, 1997), a peptide (U.S. Pat. Nos. 6,127,339 and5,574,172), a glycosaminoglycan (U.S. Pat. No. 6,106,866), a fatty acid(U.S. Pat. No. 5,994,392), a fatty emulsion (U.S. Pat. No. 5,651,991), alipid or lipid derivative (U.S. Pat. No. 5,786,387), collagen (U.S. Pat.No. 5,922,356), a polysaccharide or derivative thereof (U.S. Pat. No.5,688,931), a nanosuspension (U.S. Pat. No. 5,858,410), a polymericmicelle or conjugate (Goldman et al., 1997 and U.S. Pat. Nos. 4,551,482,5,714,166, 5,510,103, 5,490,840, and 5,855,900), and a polysome (U.S.Pat. No. 5,922,545).

Conjugation of Targeting Ligands. Antibodies, peptides, or other ligandscan be coupled to drugs or drug carriers using methods known in the art,including but not limited to carbodiimide conjugation, esterification,sodium periodate oxidation followed by reductive alkylation, andglutaraldehyde crosslinking. See Goldman et al., 1997; Cheng, 1996; Neriet al., 1997; Nebel, 1997; Park et al., 1997; Pasqualini et al., 1997;Bauminger & Wilchek, 1980; U.S. Pat. No. 6,071,890; and European PatentNo. 0 439 095.

In addition, a targeting peptide or antibody can be recombinantlyexpressed. For example, a nucleotide sequence encoding a targetingpeptide or ligand can be cloned into adenovirus DNA encoding the H1 loopfiber, such that the targeting peptide or ligand is extracellularlypresented. An adenovirus vector so prepared can be used for guideddelivery (e.g., radiation guided delivery) of a gene therapy constructas disclosed herein. A modified adenovirus vector encoding the RGDpeptide was observed to transduce the endothelium in tumor bloodvessels.

Formulation. A therapeutic composition, a diagnostic composition, or acombination thereof, of the presently disclosed subject matter comprisesin some embodiments a pharmaceutical composition that includes apharmaceutically acceptable carrier. Suitable formulations includeaqueous and non-aqueous sterile injection solutions which can containanti-oxidants, buffers, bacteriostats, bactericidal antibiotics andsolutes which render the formulation isotonic with the bodily fluids ofthe intended recipient; and aqueous and non-aqueous sterile suspensionswhich can include suspending agents and thickening agents. Theformulations can be presented in unit-dose or multi-dose containers, forexample sealed ampoules and vials, and can be stored in a frozen orfreeze-dried (lyophilized) condition requiring only the addition ofsterile liquid carrier, for example water for injections, immediatelyprior to use. Some exemplary ingredients are SDS in the range of in someembodiments 0.1 to 10 mg/ml, in some embodiments about 2.0 mg/ml; and/ormannitol or another sugar in the range of in some embodiments 10 to 100mg/ml, in some embodiments about 30 mg/ml; and/or phosphate-bufferedsaline (PBS). Any other agents conventional in the art having regard tothe type of formulation in question can be used.

The therapeutic regimens and pharmaceutical compositions of thepresently disclosed subject matter can be used with additional adjuvantsor biological response modifiers including, but not limited to, thecytokines IFN-α, IFN-γ, IL-2, IL-4, IL-6, TNF, or other cytokineaffecting immune cells.

IV.C. Administration

Suitable methods for administration of a therapeutic composition, adiagnostic composition, or combinations thereof of the presentlydisclosed subject matter include but are not limited to intravascular,subcutaneous, or intratumoral administration. In some embodiments,intravascular administration is employed. As used herein, the phrases“intravascular administration” and “intravascular provision” refer toadministration of a composition directly into the vascular network of asubject. Techniques that can be employed for intravascularadministration of compositions are known to those of skill in the art,and include, but are not limited to intravenous administration andintraarterial administration. An exemplary method of intravascularprovision that is appropriate for rodents is tail vein administration,although it is understood that any site and method for intravascularadministration can be chosen, depending at least in part on the speciesof the subject to which the composition is to be administered. Fordelivery of compositions to pulmonary pathways, compositions can beadministered as an aerosol or coarse spray.

For therapeutic applications, a therapeutically effective amount of acomposition of the presently disclosed subject matter is administered toa subject. A “therapeutically effective amount” is an amount of thetherapeutic composition sufficient to produce a measurable biologicaltumor response (e.g., an immunostimulatory, an anti-angiogenic response,a cytotoxic response, or tumor regression). Actual dosage levels ofactive ingredients in a therapeutic composition of the presentlydisclosed subject matter can be varied so as to administer an amount ofthe active compound(s) that is effective to achieve the desiredtherapeutic response for a particular subject. The selected dosage levelwill depend upon a variety of factors including the activity of thetherapeutic composition, formulation, the route of administration,combination with other drugs or treatments, tumor size and longevity,and the physical condition and prior medical history of the subjectbeing treated. In some embodiments of the presently disclosed subjectmatter, a minimal dose is administered, and dose is escalated in theabsence of dose-limiting toxicity. Determination and adjustment of atherapeutically effective dose, as well as evaluation of when and how tomake such adjustments, are known to those of ordinary skill in the artof medicine.

For diagnostic applications, a detectable amount of a composition of thepresently disclosed subject matter is administered to a subject. A“detectable amount”, as used herein to refer to a diagnosticcomposition, refers to a dose of such a composition that the presence ofthe composition can be determined in vivo or in vitro. A detectableamount will vary according to a variety of factors, including but notlimited to chemical features of the drug being labeled, the detectablelabel, labeling methods, the method of imaging and parameters relatedthereto, metabolism of the labeled drug in the subject, the stability ofthe label (e.g. the half-life of a radionuclide label), the time elapsedfollowing administration of the drug and/or labeled antibody prior toimaging, the route of drug administration, the physical condition andprior medical history of the subject, and the size and longevity of thetumor or suspected tumor. Thus, a detectable amount can vary and can betailored to a particular application. After study of the presentdisclosure, and in particular the Examples, it is within the skill ofone in the art to determine such a detectable amount.

IV.D. Radiation Treatment

The disclosed targeting ligands are useful for guided drug delivery(e.g., radiation guided drug delivery). Targeted drug delivery to atumor in a subject can be performed by irradiating the tumor prior to,concurrent with, or subsequent to administration of a composition of thepresently disclosed subject matter. In accordance with the in vivopanning methods for discovery of the targeting ligands, the tumor isirradiated in some embodiments 0 hours to about 24 hours beforeadministration of the composition, and in some embodiments about 4 hoursto about 24 hours before administration of the composition.

Low doses of radiation can be used for selective targeting using thepeptide ligands disclosed herein. In some embodiments, the dose ofradiation comprises up to about 2 Gy ionizing radiation. Higherradiation doses can also be used, especially in the case of localradiation treatment as described hereinbelow.

Radiation can be localized to a tumor using conformal irradiation,brachytherapy, or stereotactic irradiation. The threshold dose forinductive changes can thereby be exceeded in the target tissue butavoided in surrounding normal tissues. In some embodiments, doses of atleast about 2 Gy ionizing radiation can be used, and in some embodimentsa dose of about 10 Gy to about 20 Gy ionizing radiation can be used. Fortreatment of a subject having two or more tumors, local irradiationenables differential drug administration and/or dose at each of the twoor more tumors. Alternatively, whole body irradiation can be used, aspermitted by the low doses of radiation required for targeting ofligands disclosed herein: Radiotherapy methods suitable for use in thepractice of the presently disclosed subject matter can be found inLeibel & Phillips, 1998, among other sources.

IV.E. Monitoring Distribution In Vivo

In some embodiments of the presently disclosed subject matter, adiagnostic and/or therapeutic composition for guided drug deliverycomprises a label that can be detected in vivo (e.g., radiation guideddrug delivery). The term “in vivo”, as used herein to describe imagingor detection methods, refer to generally non-invasive methods such asscintigraphic methods, magnetic resonance imaging, ultrasound, orfluorescence, each described briefly hereinbelow. The term “non-invasivemethods” does not exclude methods employing administration of a contrastagent to facilitate in vivo imaging.

The label can be conjugated or otherwise associated with a targetingligand (e.g., any one of SEQ ID NOs: 1-13, 18, 20, 22, 24-69, and71-86), a therapeutic, a diagnostic agent, a drug carrier, orcombinations thereof. Following administration of the labeledcomposition to a subject, and after a time sufficient for binding, thebiodistribution of the composition can be visualized. The term “timesufficient for binding” refers to a temporal duration that permitsbinding of the labeled agent to a radiation-induced target molecule.

Scintigraphic Imaging. Scintigraphic imaging methods include SPECT(Single Photon Emission Computed Tomography), PET (Positron EmissionTomography), gamma camera imaging, and rectilinear scanning. A gammacamera and a rectilinear scanner each represent instruments that detectradioactivity in a single plane. Most SPECT systems are based on the useof one or more gamma cameras that are rotated about the subject ofanalysis, and thus integrate radioactivity in more than one dimension.PET systems comprise an array of detectors in a ring that also detectradioactivity in multiple dimensions.

A representative method for SPECT imaging is presented in Example 2.Other imaging instruments suitable for practicing the method of thepresently disclosed subject matter, and instruction for using the same,are readily available from commercial sources. Both PET and SPECTsystems are offered by ADAC of Milpitas, Calif., United States ofAmerica, and Siemens of Hoffman Estates, Ill., United States of America.Related devices for scintigraphic imaging can also be used, such as aradio-imaging device that includes a plurality of sensors withcollimating structures having a common source focus.

When scintigraphic imaging is employed, the detectable label comprisesin some embodiments a radionuclide label, in some embodiments aradionuclide label selected from the group consisting of ¹⁸fluorine,⁶⁴copper, ⁶⁵copper, ⁶⁷gallium, ⁶⁸gallium, ⁷⁷bromine, ^(80m)bromine,⁹⁵ruthenium, ⁹⁷ruthenium, ¹⁰³ruthenium, ¹⁰⁵ruthenium, ^(99m)technetium,¹⁰⁷mercury, ²⁰³mercury, ¹²³iodine, ¹²⁴iodine, ¹²⁵iodine, ¹²⁶iodine,¹³¹iodine, ¹³³iodine, ¹¹¹indium, ¹¹³mindium, ^(99m)rhenium, ¹⁰⁵rhenium,¹⁰¹rhenium, ¹⁸⁶rhenium, ¹⁸⁸rhenium, ¹²¹mtellurium, ^(122m)tellurium,^(125m)tellurium, ¹⁶⁵thulium, ¹⁶⁷thulium, ¹⁶⁸thulium, and nitride oroxide forms derived there from. In some embodiments, the radionuclidelabel comprises ¹³¹iodine or ^(99m)Tc.

Methods for radionuclide labeling of a molecule so as to be used inaccordance with the disclosed methods are known in the art. For example,a targeting molecule can be derivatized so that a radioisotope can bebound directly to it (Yoo et al., 1997). Alternatively, a linker can beadded that to enable conjugation. Representative linkers includediethylenetriamine pentaacetate (DTPA)-isothiocyanate, succinimidyl6-hydrazinium nicotinate hydrochloride (SHNH), and hexamethylpropyleneamine oxime (HMPAO) (Chattopadhyay et al., 2001; Sagiuchi et al., 2001;Dewanjee et al., 1994; U.S. Pat. No. 6,024,938). Additional methods canbe found in U.S. Pat. No. 6,080,384; Hnatowich et al., 1996; andTavitian et al., 1998.

When the labeling moiety is a radionuclide, stabilizers to prevent orminimize radiolytic damage, such as ascorbic acid, gentisic acid, orother appropriate antioxidants, can be added to the compositioncomprising the labeled targeting molecule.

Magnetic Resonance Imaging (MRI). Magnetic resonance image-basedtechniques create images based on the relative relaxation rates of waterprotons in unique chemical environments. As used herein, the term“magnetic resonance imaging”. refers to magnetic source techniquesincluding convention magnetic resonance imaging, magnetization transferimaging (MTI), proton magnetic resonance spectroscopy (MRS),diffusion-weighted imaging (DWI) and functional MR imaging (fMRI). SeeRovaris et al., 2001; Pomper & Port, 2000; and references cited therein.

Contrast agents for magnetic source imaging include but are not limitedto paramagnetic or superparamagnetic ions, iron oxide particles(Weissleder et al., 1992; Shen et al., 1993), and water-soluble contrastagents. Paramagnetic and superparamagnetic ions can be selected from thegroup of metals including iron, copper, manganese, chromium, erbium,europium, dysprosium, holmium and gadolinium. Preferred metals are iron,manganese and gadolinium; most preferred is gadolinium.

Those skilled in the art of diagnostic labeling recognize that metalions can be bound by chelating moieties, which in turn can be conjugatedto a therapeutic agent in accordance with the methods of the presentlydisclosed subject matter. For example, gadolinium ions are chelated bydiethylenetriaminepentaacetic acid (DTPA). Lanthanide ions are chelatedby tetraazacyclododocane compounds. See U.S. Pat. Nos. 5,738,837 and5,707,605. Alternatively, a contrast agent can be carried in a liposome(Schwendener, 1992).

Images derived used a magnetic source can be acquired using, forexample, a superconducting quantum interference device magnetometer(SQUID, available with instruction from Quantum Design of San Diego,Calif., United States of America). See U.S. Pat. No. 5,738,837.

Ultrasound. Ultrasound imaging can be used to obtain quantitative andstructural information of a target tissue, including a tumor.Administration of a contrast agent, such as gas microbubbles, canenhance visualization of the target tissue during an ultrasoundexamination. Preferably, the contrast agent can be selectively targetedto the target tissue of interest, for example by using a peptide forguided drug delivery (e.g., radiation guided drug delivery) as disclosedherein. Representative agents for providing microbubbles in vivo includebut are not limited to gas-filled lipophilic or lipid-based bubbles(e.g., U.S. Pat. Nos. 6,245,318, 6,231,834, 6,221,018, and 5,088,499).In addition, gas or liquid can be entrapped in porous inorganicparticles that facilitate microbubble release upon delivery to a subject(U.S. Pat. Nos. 6,254,852 and 5,147,631).

Gases, liquids, and combinations thereof suitable for use with thepresently disclosed subject matter include air; nitrogen; oxygen; iscarbon dioxide; hydrogen; nitrous oxide; an inert gas such as helium,argon, xenon or krypton; a sulphur fluoride such as sulphurhexafluoride, disulphur decafluoride or trifluoromethylsulphurpentafluoride; selenium hexafluoride; an optionally halogenated silanesuch as tetramethylsilane; a low molecular weight hydrocarbon (e.g.containing up to 7 carbon atoms), for example an alkane such as methane,ethane, a propane, a butane or a pentane, a cycloalkane such ascyclobutane or cyclopentane, an alkene such as propene or a butene, oran alkyne such as acetylene; an ether; a ketone; an ester; a halogenatedlow molecular weight hydrocarbon (e.g. containing up to 7 carbon atoms);or a mixture of any of the foregoing. Halogenated hydrocarbon gases canshow extended longevity, and thus are preferred for some applications.Representative gases of this group include decafluorobutane,octafluorocyclobutane, decafluoroisobutane, octafluoropropane,octafluorocyclopropane, dodecafluoropentane, decafluorocyclopentane,decafluoroisopentane, perfluoropexane, perfluorocyclohexane,perfluoroisohexane, sulfur hexafluoride, and perfluorooctaines,perfluorononanes; perfluorodecanes, optionally brominated.

Attachment of targeting ligands to lipophilic bubbles can beaccomplished via chemical crosslinking agents in accordance withstandard protein-polymer or protein-lipid attachment methods (e.g., viacarbodiimide (EDC) or thiopropionate (SPDP)). To improve targetingefficiency, large gas-filled bubbles can be coupled to a targetingligand using a flexible spacer arm, such as a branched or linearsynthetic polymer (U.S. Pat. No. 6,245,318). A targeting ligand can beattached to the porous inorganic particles by coating, adsorbing,layering, or reacting the outside surface of the particle with thetargeting ligand (U.S. Pat. No. 6,254,852).

A description of ultrasound equipment and technical methods foracquiring an ultrasound dataset can be found in Coatney, 2001; Lees,2001; and references cited therein.

Fluorescent Imaging. Non-invasive imaging methods can also comprisedetection of a fluorescent label. A drug comprising a lipophiliccomponent (therapeutic agent, diagnostic agent, vector, or drug carrier)can be labeled with any one of a variety of lipophilic dyes that aresuitable for in vivo imaging. See e.g. Fraser, 1996; Ragnarson et al.,1992; and Heredia et al., 1991. Representative labels include but arenot limited to carbocyanine and aminostyryl dyes, preferably long chaindialkyl carbocyanines (e.g., DiI, DiO, and DiD available from MolecularProbes Inc. of Eugene, Oreg., United States of America) anddialkylaminostyryl dyes. Lipophilic fluorescent labels can beincorporated using methods known to one of skill in the art. For exampleVYBRANT™ cell labeling solutions are effective for labeling of culturedcells of other lipophilic components (Molecular Probes Inc. of Eugene,Oreg., United States of America). Preparation of liposomes comprising atargeting ligand and a DiI detectable label are described in Example 1.

A fluorescent label can also comprise sulfonated cyanine dyes, includingCy5.5 and Cy5 (available from Amersham of Arlington Heights, Ill.,United States of America), IRD41 and IRD700 (available from Li-Cor, Inc.of Lincoln, Nebr.), NIR-1 (available from Dejindo of Kumamoto, Japan),and LaJolla Blue (available from Diatron of Miami, Fla., United Statesof America). See also Licha et al., 2000; Weissleder et al., 1999; andVinogradov et al., 1996.

In addition, a fluorescent label can comprise an organic chelate derivedfrom lanthanide ions, for example fluorescent chelates of terbium andeuropium (U.S. Pat. No. 5,928,627). Such labels can be conjugated orcovalently linked to a drug as disclosed therein.

For in vivo detection of a fluorescent label, an image is created usingemission and absorbance spectra that are appropriate for the particularlabel used. The image can be visualized, for example, by diffuse opticalspectroscopy. Additional methods and imaging systems are described inU.S. Pat. Nos. 5,865,754; 6,083,486; and 6,246,901, among other places.

IV.F. In Vitro Detection

The presently disclosed subject matter further provides methods fordiagnosing a tumor, wherein a tumor sample or biopsy is evaluated invitro. In some embodiments, a targeting ligand of the presentlydisclosed subject matter comprises a detectable label such as afluorescent, epitope, or radioactive label, each described brieflyhereinbelow.

Fluorescence. Any detectable fluorescent dye can be used, including butnot limited to FITC (fluorescein isothiocyanate), FLUOR X™, ALEXAFLUOR®, OREGON GREEN®, TMR (tetramethylrhodamine), ROX (X-rhodamine),TEXAS RED®, BODIPY® 630/650, and Cy5 (available from Amersham PharmaciaBiotech of Piscataway, N.J., United States of America, or from MolecularProbes Inc. of Eugene, Oreg., United States of America).

A fluorescent label can be detected directly using emission andabsorbance spectra that are appropriate for the particular label used.Common research equipment has been developed for in vitro detection offluorescence, including instruments available from GSI Lumonics(Watertown, Mass., United States of America) and Genetic MicroSystemsInc. (Woburn, Mass., United States of America). Most of the commercialsystems use some form of scanning technology with photomultiplier tubedetection. Criteria for consideration when analyzing fluorescent samplesare summarized by Alexay et al., 1996.

Detection of an Epitope. If an epitope label has been used, a protein orcompound that binds the epitope can be used to detect the epitope. Arepresentative epitope label is biotin, which can be detected by bindingof an avidin-conjugated fluorophore, for example avidin-FITC, asdescribed in Example 7. Alternatively, the label can be detected bybinding of an avidin-horseradish peroxidase (HRP) streptavidinconjugate, followed by colorimetric detection of an HRP enzymaticproduct. The production of a colorimetric or luminescentproduct/conjugate is measurable using a spectrophotometer orluminometer, respectively.

Autoradiographic Detection. In the case of a radioactive label (e.g.,¹³¹I or ^(93m)Tc) detection can be accomplished by conventionalautoradiography or by using a phosphorimager as is known to one of skillin the art. A preferred autoradiographic method employs photostimulableluminescence imaging plates (Fuji Medical Systems of Stamford, Conn.,United States of America). Briefly, photostimulable luminescence is thequantity of light emitted from irradiated phosphorous plates followingstimulation with a laser during scanning. The luminescent response ofthe plates is linearly proportional to the activity (Amemiya et al.,1988; Hallahan et al., 2001b).

V. Identification of a Radiation-Induced Target Molecule

Targeting ligands obtained using the methods disclosed herein can beused to identify and/or isolate a target molecule that is recognized bythe targeting ligand. Representative methods include affinitychromatography, biotin trapping, and two-hybrid analysis, each describedbriefly hereinbelow.

Affinity Chromatography. A representative method for identification of aradiation-induced target molecule is affinity chromatography. Forexample, a targeting ligand as disclosed herein can be linked to a solidsupport such as a chromatography matrix. A sample derived from anirradiated tumor is prepared according to known methods in the art, andsuch sample is provided to the column to permit binding of a targetmolecule. The target molecule, which forms a complex with the targetingligand, is eluted from the column and collected in a substantiallyisolated form. The substantially isolated target molecule is thencharacterized using standard methods in the art. See Deutscher, 1990.

Biotin Trapping. A related method employs a biotin-labeled targetingligand such that a complex comprising the biotin-labeled targetingligand bound to a target molecule can be purified based on affinity toavidin, which is provided on a support (e.g., beads, a column). Atargeting ligand comprising a biotin label can be prepared by any one ofseveral methods, including binding of biotin maleimide[3-(N-maleimidylpropionyl)biocytin] to cysteine residues of a peptideligand (Tang & Casey, 1999), binding of biotin to a biotin acceptordomain, for example that described in K. pneumoniae oxaloacetatedecarboxylase, in the presence of biotin ligase (Julien et al., 2000),attachment of biotin amine to reduced sulfhydryl groups (U.S. Pat. No.5,168,037), and chemical introduction of a biotin group into a nucleicacid ligand, (Carninci et al., 1996). In some embodiments, abiotin-labeled targeting ligand and the unlabeled same target ligandshow substantially similar binding to a target molecule.

Two-Hybrid Analysis. As another example, targeting ligands can be usedto identify a target molecule using a two-hybrid assay, for example ayeast two-hybrid or mammalian two-hybrid assay. In one embodiment of themethod, a targeting ligand is fused to a DNA binding domain from atranscription factor (this fusion protein is called the “bait”).Representative DNA-binding domains include those derived from GAL4,LEXA, and mutant forms thereof. One or more candidate target moleculesis fused to a transactivation domain of a transcription factor (thisfusion protein is called the “prey”). Representative transactivationdomains include those derived from E. coli B42, GAL4 activation domainII, herpes simplex virus VP16, and mutant forms thereof. The fusionproteins can also include a nuclear localization signal.

The transactivation domain should be complementary to the DNA-bindingdomain, meaning that it should interact with the DNA-binding domain soas to activate transcription of a reporter gene comprising a bindingsite for the DNA-binding domain. Representative reporter genes enablegenetic selection for prototrophy (e.g. LEU2, HIS3, or LYS2 reporters)or by screening with chromogenic substrates (lacZ reporter).

The fusion proteins can be expressed from a same vector or differentvectors. The reporter gene can be expressed from a same vector as eitherfusion protein (or both proteins), or from a different vector. The bait,prey, and reporter genes are co-transfected into an assay cell, forexample a microbial cell (e.g., a bacterial or yeast cell), aninvertebrate cell (e.g., an insect cell), or a vertebrate cell (e.g., amammalian cell, including a human cell). Cells that display activity ofthe encoded reporter are indicative of a binding interaction between thepeptide and the candidate target molecule. The protein encoded by such aclone is identified using standard protocols known to one of skill inthe art.

Additional methods for yeast two-hybrid analysis can be found in Brent &Finley, 1997; Allen et al., 1995; Lecrenier et al., 1998; Yang et al.,1995; Bendixen et al., 1994; Fuller et al., 1998; Cohen et al., 1998;Kolonin & Finley, 1998; Vasavada et al., 1991; Rehrauer et al., 1996;and Fields & Song, 1989.

Mass Spectroscopy. MALDI-MS can be used to identify radiation-inducedneoantigens that are well suited for immunoconjugate-mediated drugdelivery. These include antigens that are not expressed in normalvasculature, but are inducible and tethered within tumor blood vesselsand stroma. The host components of tumors (vasculature and stroma)respond to ionizing radiation with physiologic responses that occurwithin most if not all tumors. These include responses to oxidativestress and tissue injury such as receptor and enzyme activation. Theresponse in vasculature of heterotopic tumors implanted into mice isdescribed herein.

Novel radiation-induced neoantigens can also be identified by analyzingthe response of human head and neck squamous cell carcinoma (HNSCC) frombiopsies of tumors following irradiation and characterizing theproteomic response to irradiation within both microvasculature andstroma. For example, the response of stroma and endothelium followingirradiation of tumors can be analyzed to detect sites of apoptosis usingterminal deoxynucleotidyl transferase-mediated nick end labeling (TUNEL)staining. Using this approach, it was observed that irradiated tumorendothelial respond with apoptosis which provides neoantigenic targetsfor drug delivery.

EXAMPLES

The following Examples have been included to illustrate modes of thepresently disclosed subject matter. These Examples illustrate standardlaboratory practices of the co-inventors. In light of the presentdisclosure and the general level of skill in the art, those of skillwill appreciate that the following Examples are intended to be exemplaryonly and that numerous changes, modifications, and alterations can beemployed without departing from the scope of the presently disclosedsubject matter.

Example 1 Radiation Guided Delivery of Fibrinogen-Conjugated Liposomesand Microspheres

Preparation of Radiolabeled Microspheres. Albumin microspheres (Martodamet al., 1979) were resuspended using 10 ml of sterile normal saline(0.9% NaCl). One-half milliliter of the reconstituted microsphere wasadded to a 1.5 ml conical polypropylene tube previously coated withIODO-GEN® (Pierce Biotechnology, Inc., Rockford, Ill., United States ofAmerica). To this, 11.3 mCi (418 megabecquerel (MBq)) of ¹³¹I (DuPontPharmaceuticals, Wilmington, Del., United States of America) was addedin approximately 11 μl of saline and allowed to incubate at roomtemperature for 30 minutes. Following incubation, the microspheres weretransferred to a 15 ml sterile centrifuge tube, diluted to 10 ml withnormal saline and centrifuged at 1,500 g for seven minutes. Thesupernatant was removed and discarded. The microspheres were washed oneadditional time with 10 ml of normal saline and centrifuged. Themicrospheres were suspended in 2 ml of normal saline for injection.Final yield was 4.8 mCi (177.6 MBq) of radioiodinated microspheres in 2ml saline. Radiochemical yield was 42.4%.

Preparation of Fibrinogen-Conjugated Liposomes. The Lipophilic SHreactive reagent with a long spacing arm was synthesized frommaleimide-PEG 2000-NSH ester (Prochem Chemicals, High Point, N.C.,United States of America), dioleoylphosphatidylethanolanime (DOPE,available from AVANTI® Polar Lipids, Inc., Alabaster, Ala., UnitedStates of America) and triethylamine in chloroform (1:1:1.5). Resultingmaleimide-PEG 2000-DOPE was purified by flash column. Under stirring, toa solution of fibrinogen (2 mg/ml) in 0.01M HEPES 0.15 NaCl bufferpH7.9, containing 10 mM EDTA and 0.08% NaN₃ was added in 5-fold excessof freshly prepared Traut's reagent (2-iminothiolane hydrochloride) inthe same buffer. The reaction was allowed to proceed for 30 minutes at0° C.

SH-fibrinogen was purified using a PD-10 desalting and buffer exchangecolumn (Amersham Pharmacia Biotech, Piscataway, N.J., United States ofAmerica). PEG 2000-PE, cholesterol, Dipalmitoyl phosphocholine (AVANTI®Polar Lipids, Inc. of Alabaster, Ala., United States of America), DiI(lipid fluorescent marker available from Molecular Probes, Eugene,Oreg., United States of America), and maleimide-PEG-2000ADOPE weredissolved in chloroform and mixed at a molar ratio of 10:43:43:2:2,respectively, in a round bottom flask. The organic solvent was removedby evaporation followed by desiccation under vacuum for 2 hours.Liposomes were prepared by hydrating the dried lipid film in PBS at alipid concentration of 10 mM. The suspension was then sonicated 3×5minutes, or until the solution appeared clear, to form unilamellarliposomes of 100 nM in diameter. To conjugate thiolated fibrinogen tomateimide containing liposomes, prepared vesicles and thiolated proteinwere mixed in 10 mm HEPES, 0.15 M NaCl and EDTA pH 6.5. The finalconcentrations for proteins and liposomes were 0.25 g/L and 2.5 mM,respectively. The peptide/liposome mixture was incubated for 18 hours atroom temperature. Vesicles were then separated from unconjugated peptideusing a SEPHAROSE™ 4B-CL filtration column (Amersham Pharmacia Biotechof Piscataway, N.J., United States of America).

Liposomes were fluorescently labeled with DiI fluorescent marker(Molecular Probes, Inc., Eugene, Oreg., United States of America)according to the manufacturer's instructions. Labeled liposomes wereadministered by tail vein injection to tumor bearing mice. Tumors weretreated with 4 Gy either prior to administration or after administrationof fibrinogen-liposome conjugates. Tumors were fixed and sectioned at 24hours following irradiation. Fluorescence was imaged by ultravioletmicroscopy (100×).

Image Analysis. Tumor bearing mice were imaged at one hour and 24 hourspost-administration of radiolabeled proteins. Planar pinhole gammacamera imaging was performed on a single-head gamma camera (HELIX® modelfrom General Electric Medical Systems of Milwaukee, Wis., United Statesof America) using a cone-shaped pinhole collimator with a 4 mm diameterTungsten aperture. Pinhole collimation offers the advantage of improvedphoton detection efficiency (sensitivity) and spatial resolution whencompared with conventional, parallel multi-hole collimators. Pinholeplanar imaging with a small source-aperture separation can providehigh-resolution images combined with large magnification. Each scanconsisted of a 180 second acquisition (256×256 acquisition matrix) witha 10% energy window centered on 364 keV. The source-aperture separationwas 6.0 cm.

Prior to imaging analysis in animals, a uniform ¹³¹I disk source wasimaged in order to measure the angular dependence of the pinholecollimator—gamma camera system detection efficiency with distance fromthe center of the pinhole. Angular sensitivity, normalized to 1.0 at thecenter of the pinhole, was then used to scale the mouse data in order tocorrect image counts for this geometrical effect. A calibration sourceof known ¹³¹I activity was also scanned at a 6.0 cm source-apertureseparation distance in order to measure system sensitivity along thecenter of the pinhole.

Peptide biodistribution data was assessed using two measures: (1)tumor-to-background ratio (T/B) of observed activity; and (2) tumoruptake activity in μCi. Both types of data were obtained usingregion-of-interest (ROI) analysis. For both measurements an 11×11 ROIwas used to determine mean counts within the tumor (σ_(T)) and at fivedifferent locations within the mouse background (σ_(B)). These readingswere scaled to account for geometric sensitivity and the ratio of tumoruptake to total animal uptake (R) was computed according to therelation,

$R = {\frac{\sigma_{T}}{\left( {\sigma_{T} + \sigma_{B}} \right)}.}$

Activity uptake in the tumor was then approximated by the product of theamount of activity administered into the animal multiplied by the valueobtained for R above. Tumor-background ratios were determined accordingto the general expression:

$\left( \frac{T}{B} \right) = {\frac{\sigma_{T}}{\sigma_{B}}.}$

Fibrinogen Coated Microsphere Localize to Irradiated Tumors.

Fibrinogen-coated microspheres were radiolabeled with ¹³¹I andadministered by tail vein injection into tumor bearing mice, and tumorswere irradiated with 6 Gy. The specificity of fibrinogen-coated albuminwas determined by measuring the intensity of gamma detection withinregions of interest (ROI) and well counts of tumor and other tissues. Inanimals receiving localized radiation at the tumor site, 90% of themeasured radioactivity was localized to the tumor, and 10% of theradioactivity was diffusely distributed throughout the entire animalmodel. In untreated controls, 10% of radioactive counts were localizedto the tumor (p<0.001).

During optimization studies, tumors were irradiated immediately beforeor immediately after tail vein injection. Both schedules were effectivein achieving ¹³¹I-fibrinogen-coated microsphere binding. However, tumorirradiation subsequent to microsphere administration achieved increasedtargeting specificity when compared to tumors irradiated prior tomicrosphere administration. Microspheres lacking the fibrinogen liganddid not bind irradiated tumors.

To quantify a level of preferential binding of fibrinogen-coatedmicrospheres in irradiated tumors, data were normalized based onbackground levels of radiation. Fibrinogen-coated microspheres were100-fold more abundant in irradiated tumors compared to non-tumorcontrol tissues. By contrast, microspheres lacking the fibrinogen ligandwere detected at similar levels in tumor and non-tumor control tissues.

To determine whether fibrinogen-conjugated microspheres bind irradiatednon-tumor control tissues, the entire hind quarters of mice bearing hindlimb tumors were irradiated, and radiolabeled fibrinogen-coatedmicrospheres were administered immediately after irradiation. Wellcounts of all tissues were performed at 24 hours after irradiation. 90%of radioactive counts were detected in the tumor. By contrast, 2% ofradioactive counts were detected in irradiated non-tumor control tissue,demonstrating selective targeting of fibrinogen-coated microspheres toirradiated tumors.

Fibrinogen-Liposome Conjugates Localize to Irradiated Tumors.

Fibrinogen-conjugated, fluorescently labeled liposomes were administeredby tail vein into mice bearing tumors on both hind limbs. The righttumor was treated with radiation and the left tumor served as theuntreated control. Untreated control tumors showed nofibrinogen-liposome conjugate binding whereas tumors irradiatedimmediately before or immediately after tail vein injection showedfibrinogen adhesion in blood vessels. The fluorescent marker wasobserved within the vascular lumen of tumor microvasculature.

Studies using radiolabeled fibrinogen-conjugated liposomes gave similarresults. When liposomes were administered after tumor irradiation, 89%of fibrinogen-coated liposomes localized to tumors. When liposomes wereadministered immediately prior to tumor irradiation, 69% of liposomesshowed tumor localization. By contrast, in untreated controls, abackground level of 9% of fibrinogen-coated liposomes localized to thetumor.

Example 2 Clinical Trials of Radiation-Guided Delivery Using a PeptideLigand Ligand Preparation and Administration

Biapcitide (ACUTECT® available from Diatide, Inc., Londonderry, N.H.,United States of America) is a synthetic peptide that binds toGP-IIb/IIIa receptors on activated platelets (Hawiger et al., 1989;Hawiger & Timmons, 1992). Biapcitide was labeled with ^(99m)Tc inaccordance with a protocol provided by Diatide Inc.

Reconstituted ^(99m)Tc-labeled biapcitide was administered to patientsat a dose of 100 mcg of biapcitide radiolabeled with 10 mCi of ^(99m)Tc.Patients received ^(99m)Tc-labeled biapcitide intravenously immediatelyprior to irradiation. Patients were then treated with 10 Gy or more.Patients underwent gamma camera imaging prior to irradiation and 24hours following irradiation. Following planar image acquisition, thosepatients showing uptake in irradiated tumors underwent tomographicimaging using SPECT and repeat imaging at 24 hours. Patients showing nouptake on planer images during this 24-hour time frame had no furtherimaging. Each patient had an internal control, which consisted of abaseline scan immediately following administration of ^(99m)Tc-labeledbiapcitide.

Patients were treated with X-irradiation ranging from 4 to 18 MV photonusing external beam linear accelerator at Vanderbilt University.Appropriate blocks, wedges, and bolus to deliver adequate dose to theplanned target volume was utilized. The site of irradiation, treatmentintent and normal tissue considerations determined the radiation dosageand volume. When stereotactic radiosurgery was used, the dose wasprescribed to the tumor periphery.

Image Analysis. Image acquisition consisted of both planar and singlephoton emission computed tomography (SPECT) studies. Planar studies wereperformed on a dual-head gamma camera (Millenium VG—Variable Geometrymodel available from General Electric Medical Systems of Milwaukee,Wis., United States of America) equipped with low energy high-resolution(LEUR) collimators. This type of collimator represents a compromisebetween sensitivity (photon counting efficiency) and image resolution.Planar nuclear medicine images were acquired with a 256×256 acquisitionmatrix (pixel size approximately 0.178 cm/pixel) for 10 minutes. Inorder to maximize collimator-gamma camera system sensitivity thesource-to-detector surface distance was minimized to the extent thatpatient geometry allows. The spatial distribution of fibrinogen withinthe planar image was measured using region-of-interest (ROI) analysis.Two different size ROI's (5×5 pixel, and 15×15 pixel) was used in boththe tumor and surrounding organs and tissues in the patient. Therationale for using ROIs with different dimensions is to be able toquantify image counts while at the same time isolating any possibleinfluence of ROI size on the results. Tumor-to-background ratios werecomputed as the ratio of average counts in the tumor region divided byaverage counts in surrounding organs and tissues, each corrected forbackground. Background counts was determined based on ROI analysis of aseparate planar acquisition performed in the absence of a radioactivesource.

Three-dimensional nuclear medicine SPECT examinations were performedusing the same dual-head gamma camera system. Each SPECT study compriseda 360 scan acquired with a step-and-shoot approach utilizing thefollowing acquisition parameters: three increments between views, a256×256×64 acquisition matrix, LEUR collimation and 60 seconds per view.Images were reconstructed using analytical filtered back-projection andstatistical maximum likelihood techniques with photon attenuationcorrection and post-reconstruction deconvolution filtering forapproximate detector response compensation. In this case, correction forbackground consisted of subtracting counts acquired in a single60-second planar view from all views of the SPECT projection data priorto image reconstruction. SPECT tumor-to-background ratios were computedusing quantitative ROI techniques identical to the planar studies.

Results. Administration of a ^(99m)Tc-labeled biapcitide, an RGD peptidemimetic, immediately prior to radiation resulted in tumor binding in 4of 4 patients (Hallahan et al., 2001a). Two patients among this grouphad second neoplasms that were not treated with radiation, and bindingof ^(99m)Tc-labeled biapcitide was not observed in the untreated tumor.Administration of the ^(99m)Tc-labeled biapcitide within one hourfollowing radiation also failed to show localization of the targetingmolecule to the tumor (Hallahan et al., 2001a).

Example 3 Response of Tumor Blood Vessels to Ionizing Radiation

To determine the response of tumor blood vessels to ionizing radiation,a tumor vascular window and Doppler sonography were used to measure thechange in tumor blood vessels (Donnelly et al., 2001; Geng et al.,2001). Tumors implanted into the window model developed blood vesselswithin 1 week. Tumors were then treated with radiation and the responseof blood vessels was imaged by use of light microscopy. Radiation dosesin the range of 2-3 Gy increased the vascularity within tumors. Incontrast, larger doses of radiation such as 6 Gy reduced tumorvascularity.

Established tumors were studied to determine whether there is adose-dependent change in blood flow following irradiation. Tumors in thehind limb were grown to approximately 1 cm in diameter. Blood flowwithin tumors was measured by use of power Doppler (Donnelly et al.,2001). Tumors were treated with 3 Gy or 6 Gy ionizing radiation; andchanges in tumor blood flow were measured using power Dopplersonography. A radiation dose of 3 Gy achieved an increase in tumor bloodflow. In contrast, radiation doses of 6 Gy or higher markedly reducedtumor blood flow.

Example 4 Preparation of a Recombinant Peptide Library in Phage

A population of DNA fragments encoding recombinant peptide sequences wascloned into the T7 SELECT™ vector (Novagen, Madison, Wis., United Statesof America). Cloning at the EcoR I restriction enzyme recognition siteplaces the recombinant peptide in-frame with the 10B protein such thatthe peptide is displayed on the capsid protein. The resulting readingframe requires an AAT initial codon followed by a TCX codon.

The molar ratio between insert and vector was 1:1. Size-fractionatedcDNA inserts were prepared by gel filtration on sepharose 4B and rangedfrom 27 base pairs to 33 base pairs cDNAs were ligated by use of the DNAligation kit (Novagen). Recombinant T7 DNA was packaged according to themanufacturer's instructions and amplified prior to biopanning in animaltumor models. The diversity of the library was 10⁷.

Example 5 In Vivo Panning for Peptide Ligands to Radiation-InducedMolecules

GL261 murine glioma cells and Lewis lung carcinoma cells were implantedinto the hind limb of C57BL6 mice (Hallahan et al., 1995b; Hallahan etal., 1998; Hallahan & Virudachalam, 1999).

To determine the optimal time at which peptides bind within tumors,phage were administered at 1 hour before, at 1 hour after, and at 4hours after irradiation of both LLC and GL261 tumors. Phage wererecovered from tumors when administered 4 hours after irradiation. Phageadministered 1 hour before or 1 hour after irradiation were notrecovered from tumors. These data indicate that the optimal time ofadministration is beyond 1 hour after irradiation.

For in vivo panning, tumors were irradiated with 3 Gy and approximately10¹⁰ phage (prepared as described in Example 4) were administered bytail vein injection into each of the tumor bearing mice at 4 hoursfollowing irradiation. Tumors were recovered at one hour followinginjection and amplified in BL21 bacteria. Amplified phage were pooledand re-administered to a tumor-bearing mouse following tumorirradiation. The phage pool was sequentially administered to a total of6 animals. As a control, wild type phage lacking synthetic peptideinserts were identically administered to a second experimental group ofanimals.

To determine the titer of phage binding in a tumor or in normal tissue,recovered phage were amplified in BL21 bacteria. Bacteria were platedand the number of plaques present were counted. To determine the totalphage output per organ, the number of plaque forming units (PFU) on eachplate was divided by the volume of phage plated and the weight of eachorgan. Normal variation was observed as a 2-fold difference in PFU.

In the present study, background binding within tumor blood vessels wasapproximately 10⁴ phage. Phage that bound to the vasculature withinirradiated tumors show enrichment in the tumor relative to other organsand enrichment in the irradiated tumor relative to the control phagewithout DNA insert. Phage that home to irradiated tumors showed abackground level of binding in control organs that was lower thancontrol phage without DNA insert.

Following 6 rounds of in vivo panning, fifty recombinant phage peptidesthat bound within irradiated tumors were randomly selected for furtheranalysis. The nucleic acid sequence encoding recombinant phage wasamplified by PCR using primers set forth as SEQ ID NOs: 14-15 (availablefrom Novagen of Madison, Wis., United States of America). An individualphage suspension was used as template. Amplified peptides were sequencedusing an ABI PRISM® 377 sequencer (Applied Biosystems, Foster City,Calif., United States of America). The sequences of the encoded peptidesare listed in Table 1. Several conserved subsequences were deduced fromthe recovered peptides and are presented in Table 2.

Peptide sequences recovered from both tumor types include NHVGGSSV (SEQID NO: 1), NSLRGDGSSV (SEQ ID NO: 2), and NSVGSRV (SEQ ID NO: 4).Of thepeptide sequences recovered from 6 irradiated tumors, 56% had thesubsequence GSSV (SEQ ID NO: 5), 18% had the sequence RGDGSSV (SEQ IDNO: 6), and 4% had the sequence GSRV (SEQ ID NO: 7). Approximately 22-40of 10⁶ injected phage were recovered from irradiated tumors having apeptide insert comprising the subsequence GSSV (SEQ ID NO: 5). Bycontrast, no phage were from irradiated tumors following administrationof 10⁶ wild type phage.

TABLE 1 Peptides Identified by Invivo Panning of LLC and GL261 TumorsNumber of Phage Number of Phage Recovered from Recovered from LLC tumors  GL261 tumors Peptide Sequence  (Frequency)  (Frequency)NHVGGSSV  7 (28%) 12 (48%) (SEQ ID NO: 1) NSLRGDGSSV  7 (28%) 2 (8%)(SEQ ID NO: 2) NSVRGSGSGV  7 (28%) 0 (SEQ ID NO: 3) NSVGSRV  1 (4%)  3 (12%) (SEQ ID NO: 4) Unique Sequences  3 (12%)  8 (32%)

TABLE 2 Conserved Motifs within Peptides Identified by In vivo PanningConserved Sequence Frequency of Recovery GSSV (SEQ ID NO: 13) 56%GSXV (SEQ ID NO: 8) 78% NSXRGXGS (SEQ ID NO: 9) 32% NSV (SEQ ID NO: 10)22% NSXR (SEQ ID NO: 11) 32% NXVG (SEQ ID NO: 12) 46%

Example 6 Peptide Targeting in Additional Tumors

The binding properties of phage encoding NHVGGSSV (SEQ ID NO: 1),NSLRGDGSSV (SEQ ID NO: 2), NSVRGSGSGV (SEQ ID NO: 3), and NSVGSRV (SEQID NO: 4) were additionally characterized in a B16F0 melanoma model.Peptides set forth as SEQ ID NOs: 1 and 2 bound within the melanoma,lung carcinoma, and glioma tumor models. SEQ ID NO: 3 bound withinglioma and melanoma, and SEQ ID NO: 4 bound within lung carcinoma andglioma.

Example 7 Characterization of Peptide Binding to Irradiated Tumors

To determine where recombinant peptides bind in tumor blood vessels, thebiodistribution of biotinylated peptides was assessed. Tumors weretreated with 3 Gy and biotinylated peptides were administered by tailvein at 4 hours following irradiation. Tumors were recovered 30 minutesfollowing administration of biotinylated peptides. Tumors were snapfrozen and sectioned on a cryostat. Frozen sections were then incubatedwith Avidin-FITC (fluorescein isothiocyante) and imaged by fluorescentmicroscopy. Recombinant peptides (for example, those set forth inTable 1) were observed to bind the vascular endothelium within tumorblood vessels.

The anti-α_(2b)β₃ monoclonal antibody was administered by tail vein todetermine whether this receptor is required for recombinant phagebinding in irradiated tumors. Phage encoding SLRGDGSSV (SEQ ID NO: 5) onthe capsid protein were injected immediately after blocking antibody orcontrol antibody. Phage were recovered from the tumor and controlsorgans and quantified by plaque formation. Radiation induced a 4-foldincrease in phage binding in tumor. Blocking antibody eliminatedinduction of phage binding, while control antibody to P-selectin (onactivated platelets) did not reduce phage binding. Thus, the tumorbinding activity of targeting peptide SLRGDGSSV (SEQ ID NO: 5) isdependent on its interaction with the α_(2b)β₃ receptor.

Example 8 Production of a Phage-Displayed scFv Antibody Library

A phage-displayed antibody library was constructed based upon previouslypublished methodologies (see Pope at al., 1996). Briefly, spleens fromoutbred newborn and three-to-four week old mice and rats were used as asource of antibody-encoding genetic material to produce a library ofabout 2×10⁹ members. The antibody-encoding genetic material was clonedinto the pCANTAB phagemid vector.

The pCANTAB vector contains an amber stop codon that is locateddownstream of the scFv coding sequences and upstream of the M13 gene IIIcoding sequences. E. coli TG1 cells (a sup E strain of E. coli) containa suppressor tRNA that inserts a glutamic acid residue in response to anUAG (amber) stop codon. The amber stop codon is about 14% efficient.Therefore, the scFv antibody amino acid sequences will be fused to M13phage gene III amino acid sequences about 14% of the time, and will beproduced as a soluble, non-fusion protein about 86% of the time when thelibrary is grown in TG1 cells. In contrast, E. coli strain HB2151 doesnot contain the amber stop codon, and thus only soluble non-fused scFvwill be produced when the library is grown in HB2151.

Example 9 In Vivo Panning for Antibody Ligands to Radiation-InducedMolecules

A phage library comprising diverse single chain antibodies was preparedin M13 phage. The phage library was exposed to the radiation-inducedneoantigens P-selectin (also called CD62P; GENBANK® Accession No.NP_(—)002996) and/or platelet membrane glycoprotein IIB (also calledCD41; GENBANK® Accession Nos. P08514 and NP_(—)000410) immobilized onglass slides. Phage were selected based on antigen binding, and selectedphage were pooled as a biased library. For representative in vitropanning methods, see Fowlkes et al., 1992; Haaparanta & Huse, 1995; Jung& Pluckthun, 1997; Peter et al., 2000; Holzem at et al., 2001; Chiu etal., 2000.

Phage identified by in vitro panning were tested on Western immunoblotsto confirm binding to the P-selectin and platelet membrane glycoproteinIIB neoantigens. Phage that specifically bound P-selectin and plateletmembrane glycoprotein MB were subsequently used for in vivo panning toirradiated tumors as described in Example 5. Wild type phage were usedas internal controls. Antibodies having substantial affinity forirradiated tumors were identified by observing an increased number ofphage in the irradiated tumor when compared to a number of phage in acontrol organ (e.g., liver and lung). Phage antibodies with the greatestaffinity for tumors were identified using the formula: number of phagein irradiated tumor/number of phage in each organ.

Eight antibodies that bound P-selectin and fifteen antibodies that boundplatelet membrane glycoprotein IIB were recovered following in vivopanning to irradiated tumors. Representative targeting antibodiesidentified by this method include the single chain antibodies set forthas SEQ ID NOs: 18, 20, 22, and 24 (encoded by SEQ ID NOs: 17, 19, 21,and 23, respectively), which recognize the radiation-induced neoantigensP-selectin and platelet membrane glycoprotein IIB, respectively.

Example 10 Conformational Changes Induced in Perlecan

Mass spectrometry analysis of the samples revealed that co-culturingHMVEC cells with H460 tumor cells induced several proteins expression onthe HMVEC cells. Among them, CYR61 and perlecan had been demonstrated tobe important for tumor growth and angiogenesis. Most importantly,several proteins underwent conformational changes, by exposing some newbiotinylation sites as well as hiding some other sites forbiotinylation.

One such protein was the perlecan precursor (GENBANK® Accession Nos.P98160 and NP_(—)005520; SEQ ID NO: 70). Several subsequences of theperlecan precursor were found to undergo conformational changes uponco-culture as evidenced by the blocking of existing biotinylation sites.These subsequences are presented in Table 3.

TABLE 3 Conformational Changes Induced in Perlecan by Co-CultureAmino acids Biotinylation  of SEQ ID Site Subsequence  NO: 70 Blocked?RPEEVCGPTQFR  363-374 Yes LRFDQPDDF  542-550 No NVRYELAR  617-624 YesGMLEPVQRPDVVLVGAGY  625-642 Yes AHSVEECRCPIGY  725-737 Yes SGLSCESCDAHF 738-749 No ATATSCRPCPCPY  806-818 Yes RFSDTCFLDTDGQATCDACAPGYTGR 824-849 Yes RCESCAPGYEGNPIQPGGK  850-868 Yes CRPVNQEIVR  869-878 NoRPVNQEIVR  870-878 Yes TCESLGAGGYR 1627-1637 No AVTLECVSAGEPR 3129-3141No CSATGSPAPTIHWSK 3233-3247 Yes IAHVELADAGQYR 3542-3554 YesIAHVELADAGQY 3542-3553 Yes IAHVELADAGQYRCTATN 3542-3559 Yes AHLQVPER3654-3661 Yes VVPYFTQTPY 3662-3671 Yes NGQKRVPGSPTNL 3704-3716 NoVCVCPAGFTGSR 3868-3879 Yes SAEPLALGR 4004-4012 Yes CLCLPGFSGPR 4164-4174Yes

Additional conformational changes were identified when the co-culturedcells were irradiated with 2 Gy, as new biotinylation sites wereinduced. These changes are summarized in Table 4.

TABLE 4 Conformational Changes Inducedin Perlecan by Co-Culture and Irradiation Amino acids of New BiotinylationSubsequence SEQ ID NO: 70 Site Induced? LRFDQPDDF 542-550 NoGHTPTQPGALNQR 648-660 Yes SGLSCESCDAHF 738-749 No CRPVNQEIVR 869-878 NoTCESLGAGGYR 1627-1637 No AVTLECVSAGEPR 3129-3141 No NGQKRVPGSPTNL3704-3716 No AGLSSGFIGCVR 3810-3821 Yes GCVGEVSVNGK 4075-4085 YesCQQGSGHGIAESDW 4175-4188 Yes

Example 11 Identification of Additional Targeting Peptides by In VivoPanning

Tumors (Lewis Lung Carcinoma, LLC) were implanted into both sides ofhind limbs of C57 mice, and one side of tumor was treated with 2 Gy ofradiation when the tumors reached a size of 1 cm in diameter. Six T7phage-based random peptide libraries were screened separately byinjection through tail veins at 18 hours after the radiation, and phageswere circulated for 1 hour before the mice were sacrificed to recoverphages from the radiated tumor. The recovered phages were amplified byinfecting a bacterial host as described hereinabove, and used as inputfor the next round of biopanning.

After five rounds of in vivo biopanning, single phage clones wereisolated and the peptide sequence was deduced by sequenced the relevantfragment in the phage genome. Dozens of peptides were recovered from theirradiated tumors, with several enriched to be dominant after the finalround of biopanning. The isolated phage were purified and injected intotumor-bearing mice. Phages in tissues were visualized using an anti-T7phage antibody in conjunction with a FITC-conjugated secondary antibody.DAPI staining was used to localize the cell nucleus.

Representative data indicated that the isolated phage targeted theirradiated tumor cells by the peptide displayed on its surface. Certainof these peptide sequences are presented in SEQ ID NOs: 26-60.

Example 12 In Vitro Panning for Nuclear Targeting Peptides

T7-based linear peptides (×12, 16 and 20) were subjected for biopanningon HUVEC monolayers. After 20 hours incubation at 37° C., phagesrecovered from nuclei were amplified and used for the following round ofselection. Titration result for phages recovered from nuclei andcytoplasm in all the rounds of screening showed that some nucleus-homingphages had been enriched in the biopanning process. Phages from thethird round nucleus extraction were sequenced and are presented in SEQID NOs: 61-69.

A BLAST search indicated that the isolated sequence is close to awell-studied sequence motif which was characterized as nucleus-exportingsignature (NES). However, the cy3-labeled phage were located in HUVECnuclei, compared with localization of the control phage without thepeptide insert on cell membrane or in cytoplasm. Other proteins thatcontain a Nucleus-Export Sequence (NES) are as follows:

HIV-1 Rev LPPLERLTLD HTLV-1 Rex LSAQLYSSLSLD HSV-1 ICP27 IDMLIDLGLDLDEBV Sm LPSPL-ASLTL HSV-VP13/14 NES1 LGRVL-DVLAVM HSV-VP13/14 NES2LHTAL-ATVTLK HSV-VP13/14 NES3 LAAGLVLQRLLG MVM NS2 MTKKFGTLTI PKILALKLAGLDI MAPKK LQKKLEELEL NMD3 LAEMLEDLHI An3 LDQQFAGLDL IκBaMVKELQEIRL Cyclin B1 LCQAFSDVIL TFIIIA LPVLENLTL Consensus φX₂₋₃φX₂₋₃φXφφ = L, I, V, F or M, residues with large hydrophobic side chain. X = anyamino acid

Engeisma et al., 2004 reported two phage-displayed peptides isolatedfrom an M13 library, S0 and P0, which contained NES-like sequences andlocalized to the nuclear membrane.

S0 LARLFSALSV P0 LSSLFSGLSV Consensus LX2LFX2LSV Peptide from 17 libraryFTHALDPGQLAL

Materials and Methods Employed in Examples 13-16

Linking Compounds. Linking compounds include1,3,4,6-tetrachloro-3a,6a-diphenylglcouril (a reagent sold under theregistered trademark IODO-GEN0), and MPBA, each available from PierceBiotechnology, Inc. (Rockford, Ill., United States of America). TheIODO-GEN® reagent reacts with tyrosine residues, while MPBA reacts withcysteine residues, both of which are not on the peptide HHLGGAKQAGDV(SEQ ID NO: 16). An advantage of the IODO-GEN® reagent is that it issupplied in coated tubes and beads to eliminate contamination of theinjectable material, whereas MPBA is in powder form. Initial experimentsuse the IODO-GEN® reagent to iodinate a poly-tyrosine peptide derivativeof HHLGGAKQAGDV-SGSGS (SEQ ID NO: 26), HHLGGAKQAGDV-SGSGS-YYYYY (SEQ IDNO: 28), and additional experiments use MPBA to iodinate poly-Cys.

Preparation and Radioiodination of Peptides. An IODO-GEN®-platedreaction vessel (Pierce Biotechnology, Inc.) is rinsed with a smallamount of sterile saline to remove any loose microscopic flakes of theiodination reagent. The desired amount of carrier-free ¹²⁵I sodiumiodide, a specific activity of 100 mCi/mg protein, is added to thereaction vessel, followed by the reconstituted peptides suspension. Thereaction vessel is then sealed off and the reaction is allowed toproceed for 20 minutes at room temperature with constant gentleagitation of the reaction vessel. The iodination process is terminatedby removing the reaction mixture from the reaction vessel into acentrifugation tube. The reaction mixture is centrifuged at 3,000 rpmfor 15 minutes. The supernatant is removed and the residue isreconstituted in 5 ml sterile normal saline.

Pinhole Gamma Camera Imaging of Peptide Biodistribution. A dedicatedresearch single-head gamma camera (20 cm×40 cm active imaging area)fitted with a cone-shaped pinhole collimator is used for nuclearmedicine animal imaging experiments. The pinhole collimator, equippedwith a 4 mm aperture Tungsten insert, is used to acquire pre-treatmentand serial, post-treatment follow-up images of each animal in order todetermine the temporal distribution of peptide in vivo. Each pinholeacquisition comprises a planar view acquired for 3 minutes using a256×256 pixel acquisition matrix. In order to maximize pinholecollimator-gamma camera system sensitivity, a source-to-aperturedistance on the order of 2 cm to 5 cm is maintained. The spatialdistribution of peptide within each image is measured usingquantitative, region of interest (ROI) analysis. Two different size ROIsare used in both the tumor region and moue background in order toquantify image counts and isolate any possible influence of ROI size onquantification. A 2×2 (small) and 11×11 (large) pixel ROI are used torecord image counts in the tumor and other organs in the mouse. Theangular dependence of pinhole efficiency is measured using a flat,uniform sheet source of activity. Image counts are then corrected fordecay and this geometric effect.

Statistical Considerations. Internal controls are established in eachanimal by use of an untreated control tumor implanted on the left hindlimb and irradiation of the right hind limb tumor, as described inHallahan, 1995b and Hallahan, 1998.

Sample Size and Power Analysis. In order to calculate the statisticalsignificance of differences between groups of mice, eight mice arestudied at each time to determine statistical significance. In general,a sample size of eight per group gives about 80% of power to detect adifference of 1.5-fold standard deviations in the interesting parametersbetween two groups with a two-sided statistic equal to 5%.

Statistical Analysis Plan. Pharmacokinetic parameters are presented intabular and graphic form. Pharmacokinetic parameters such as maximalplasma concentration, time of maximal concentration, and area under theplasma concentration time curve are determined using non-compartmentalmethods. Statistical analyses are performed using the General LinearModel method of the Statistical Analysis System (SAS). If significantdifferences are indicated by the ANOVA analysis, the Waller-DuncanK-ratio t-test procedure is used for pairwise comparisons of meanpharmacokinetic parameter values.

For the single time point data, tests of hypotheses concerningcorrelation between imaging results and results are completed using thepaired t-test or Wilcoxon Signed-Rank test for the interestingcontinuous parameters or the McNemar's Chi-square test for theinteresting categorical parameters. For either count or binary multipletime points data, tests concerning correlation between imaging resultsand pharmacokinetic results are made using the Generalized EstimatingEquation (GEE) method statistical procedure for longitudinal dataanalysis with multiple observable vectors for the same subject (Diggle,1994; Liang, 1986). For continuous multiple time points data, testsconcerning correlation between groups are completed using therestricted/residual maximum likelihood (REML)-based repeated measuremodel (mixed model analysis; Jennrich, 1986) with various covariancestructure.

The statistical analyses are completed by SAS 6.12 statistical program,or SAS IML macro in this project. Computer connections, when necessary,are attained via a Novell network using the Internet Packet eXchange(IPX) protocol.

Example 13 X-Ray-Guided Drug Delivery Via Antibody Delivery Vehicles

Following platelet activation, several antigens are expressed on thesurface of platelets. Indeed, it has been observed that irradiation ofanimal tumors increases the expression of platelet antigens such asP-selectin and GPIIb/IIIa. As disclosed herein above, antibodies can beconjugated to radionuclides, cytotoxic agents, gene therapy vectors,liposomes, and other active agents. In this Example, the administrationof radioimmunoconjugate delivery vehicles against platelet antigensfollowing irradiation of tumors is disclosed.

Anti-GPIIb/IIIa antibodies (R&D Systems, Inc., Minneapolis, Minn.,United States of America) are labeled with ¹³¹I using 1000-GEN® reagent(Pierce Biotechnology, Inc., Rockford, Ill., United States of America).Labeled antibody is separated from free iodine by use of columnchromatography. Radioimmunoconjugates are injected into mice by tailvein. Hind limb tumors are implanted and treated as described hereinabove. The optimal time of administration of radioimmunoconjugates isdetermined.

In separate experiments, procoagulants such as DDAVP are alsoadministered to enhance radioimmunoconjugate binding to activatedplatelets in irradiated tumors. Mouse subjects are imaged by gammacamera as described herein above. PHOSPHORIMAGER™ plates and histologicsections with immunohistochemistry as described herein above are used tovalidate image processing. In the event that certainradioimmunoconjugates do not achieve specific activity within tumorsthat is sufficient to image or treat tumors, multiple radionuclides areincorporated into the antibody delivery vehicles.

In additional experiments, Fab′ fragments of anti-GPIIIa and anti-GPIIbantibodies are also employed in binding in a site-specific manner toirradiated tumors. It is shown herein that anti-GPIIIa antibody stainingin blood vessels following X-irradiation. There are two approaches inproducing antibodies for site-specific binding. The first is cleavage ofthe IgG antibody to form the Fab′ fragment. The second approach is theuse of phage antibodies to GPIIIa and GPIIb that are produced in theVanderbilt Cancer Center Molecular Discovery Core Laboratory usingphage-display techniques. Each of these approaches yields low molecularweight antibodies that can be efficiently produced for clinical studies.Specificities of the GPIIIa (integrin β₃) antibodies and antibodyfragments are compared to the specificities of the GPIIb antibodies andantibody fragments to establish potentially useful reagents and in thatGPIIIa is also found in α_(v)β₃.

Experimental Design. The anti-GPIIIa and anti-GPIIb antibodies (R&DSystems, Inc.) are cleaved to form the Fab′ fragment. This fragment isisolated from the Fc fragment by columns. In addition, GPIIIa protein isscreened with a phage library within the Vanderbilt Cancer CenterMolecular Discovery Core Laboratory. Antibody from phage is grown up inthe bacteria. Antibodies are then studied for binding in irradiatedtumors. Antibodies are labeled with ¹³¹I using IODO-GEN® reagent asdescribed above. The molar ratio of ¹³¹I to antibody is optimized toavoid potential reduction in the affinity of antibody binding due to¹³¹I.

Tumors are implanted and irradiated as described herein.Radio-immunoconjugates are administered immediately after irradiationusing tail vein injection. Eight mice are randomly assigned intoexperimental and control groups. Imaging and quantification of ¹³¹I areperformed as described above. Statistical analysis is performed asdescribed above.

Positive control aromas. Radiolabeled fibrinogen is administered toirradiated tumor bearing mice and compared to radioimmunoconjugates.These mice are randomly assigned into groups during the same experimentas radioimmunoconjugates.

Negative control groups. Non-irradiated control tumors are implanted inthe left hind limb of all mice. Secondly, radiolabeled anti-α_(v) andanti-human IgG antibodies are administered to tumor bearing micefollowing irradiation to verify that antibody binding to irradiatedtumors is not a generalized phenomenon.

Example 14 X-Ray-Guided Drug Delivery Targeted to Radiation-InducedNeoantigens in Blood Vessels

Radiation-induced targets for drug delivery systems will be most usefulif they are not tumor-specific. The vascular endothelium is an essentialcomponent to nearly all neoplasms. As disclosed herein above, radiationresponse is similar across a wide range of tumor types. In particular,P-selectin exocytosis, von Willebrand Factor release, and plateletaggregation are observed within all tumor blood vessels followingirradiation. In this Example, antibody delivery vehicles forX-ray-guided drug delivery to the vascular endothelium of tumors aredisclosed. Antibody delivery vehicles adhere to antigens released intothe lumen and are thus obstructed from circulating beyond the confinesof the tumor. In view of the targeting of vascular endothelium, thisExample is also illustrative of the methods of treating angiogenesis inaccordance with the presently disclosed subject matter disclosed hereinabove.

Additionally, one level of radiation-induced expression of receptors andadhesion molecules is the activation of inactive receptors followingirradiation of tumor blood vessels. Tumors in the hind limb of mice weretreated with 2 Gy ionizing radiation followed by sectioning andimmunohistochemical staining for the β₃ integrin in the tumor sections.The observed histologic pattern of staining showed that both plateletsand endothelium stain with anti-β₃ antibody after irradiation, but notprior to irradiation. Thus, therapeutic doses of irradiation (2 Gy) wereand are sufficient to induce the accumulation of integrin β₃ withintumor blood vessels within 1-4 hours of irradiation.

Hind limb tumors are implanted into mice and treated with radiation asdescribed in Hallahan et al., 1998a. Radioimmunoconjugate deliveryvehicles are prepared using anti-E-selectin and anti-P-selectinantibodies (R&D Systems, Inc.), IODO-GEN® reagent (Pierce Biotechnology.Inc.) and ¹³¹1. Radiolabeled antibodies are separated from free ¹³¹1 byuse of column chromatography. The delivery vehicles are injected viatail vein into mice with hind limb tumors following treatment withirradiation. Mice are imaged with gamma camera imaging as describedherein above. Image processing is validated by use of PHOSPHORIMAGER™plates, immunofluorescence, and immunohistochemistry as described hereinabove.

One potential limitation of this embodiment of the presently disclosedsubject matter is that anti-E-Selectin antibody binding occurs inuntreated normal tissues such as the lung. The importance of validationof the tumor specificity for radioimmunoconjugate delivery vehicles isthat the ideal radiation-induced antigens have substantially noconstitutive expression in any tissue, but prolonged expression in tumorblood vessels. Thus, pharmacokinetics and biodistribution of theanti-E-selectin and anti-P-selectin antibody delivery vehicles are alsodetermined.

Example 15 X-Ray-Guided Drug Delivery by Use of a Twelve Amino AcidSegment of the γ Subunit of Fibrinogen

This Example pertains to the use of the dodecapeptide HHLGGAKQAGDV (SEQID NO: 16), a segment of the γ subunit of fibrinogen, to achievesite-specific binding to irradiated tumors. This peptide segment of thecarboxyl terminus of the fibrinogen γ chain binds to GPIIb/IIIafollowing platelet activation. The fibrinogen binding sequence(HHLGGAKQAGDV; SEQ ID NO: 16) is sufficient for site-specificlocalization to irradiated tumors.

Observations. The peptide sequence within fibrinogen that binds to theactivated GPIIb/IIIa receptor is the dodecapeptide HHLGGAKQAGDV (SEQ IDNO: 16). To determine whether HHLGGAKQAGDV (SEQ ID NO: 16) binds inirradiated tumors, applicant utilized the peptide HHLGGAKQAGDV (SEQ IDNO: 16) linked to biotin by a serine-glycine linker(HHLGGAKQAGDV-SGSGSK-biotin; SEQ ID NO: 30). This peptide wassynthesized in the Vanderbilt University Peptide Core Lab andbiotinylated at the carboxyl terminus. The resultingHHLGGAKQAGDV-SGSGSK-biotin (SEQ ID NO: 30) was administered by tail veininjection into tumor bearing mice. B16F0 tumors in the hind limb weretreated with sham irradiation (control), 4 Gy irradiation followed byHHLGGAKQAGDV-SGSGSK-biotin (SEQ ID NO: 30) injection, orHHLGGAKQAGDV-SGSGSK-biotin (SEQ ID NO: 30) followed by tumor irradiation(4 Gy). Tumors were frozen at 4 hours and sectioned for fluorescencestaining. Avidin-FITC was incubated with tumor sections and imaged by UVmicroscopy. Avidin-FITC stained blood vessels were observed inirradiated tumors, but not in untreated control. Moreover, it was foundthat HHLGGAKQAGDV (SEQ ID NO: 16) administration prior to irradiation isa more efficient schedule of administration as compared to radiationbefore dodecapeptide administration.

Design of Iodination Experiments. Tumors are implanted and irradiated asdescribed herein above. The synthetic dodecapeptide encompassing thesequence HHLGGAKQAGDV (SEQ ID NO: 16) on the carboxyl-terminal segmentof fibrinogen γ chain binds to GPIIb/IIIa is prepared, and a peptidetail for radioiodination (SGSGS-YYYYY; SEQ ID NO: 32) is added. Thepeptide tail is commercially available from PeptidoGenic Research & Co.(Livermore, Calif., United States of America). A sample from each batchis sequenced in accordance with standard techniques for quality control.

HHLGGAKQAGDV-SGSGS-YYYYY (SEQ ID NO: 28) is labeled with ¹³¹I usingIODO-GEN® reagent as described above. When tumors are grown to 0.5 cm indiameter, the tail vein of each mouse subject is cannulated and¹³¹I-labeled HHLGGAKQAGDV-SGSGS-YYYYY (SEQ ID NO: 28) is injected. Theinjection tubing and syringe is counted after the injection to measureresidual ¹³¹I. Immediately after administration of ¹³¹I-peptide, tumorsare irradiated using techniques described herein and by Hallahan et al.,1998. Mice are imaged by gamma camera imaging at 1 and 24 hours afterirradiation. ¹³¹I-labeled HHLGGAKQAGDV-SGSGS-YYYYY (SEQ ID NO: 28)binding to tumors is quantified by gamma camera imaging and direct wellcounts from excised tumors as described above. Tissue sections of allorgans are analyzed. Eight tumor-bearing mice are randomly assigned intoeach of the experimental and control groups. Statistical considerationsare addressed as described above.

Positive control groups. Radioiodinated-fibrinogen is administered toirradiated tumor bearing mice and compared to radioiodinated-peptide.These mice are randomly assigned into groups during the same experimentas radiolabeled peptides.

Negative control groups. Non-irradiated control tumors are implanted inthe left hind limb of all mice. Secondly, radiolabeledSGSGSGSSGSGSSGSGS-YYYYY (SEQ ID NO: 33) are administered to tumorbearing mice following irradiation to verify that peptide binding toirradiated tumors is not a generalized phenomenon.

It is noted that the three-dimensional conformation of fibrinogen mightfacilitate site-specific binding to irradiated tumors. Alternatively,¹³¹I labeling might interfere with peptide binding to GPIIb/IIIa. Alonger peptide linker and fewer Tyr residues are options that areemployed in each case.

Example 16 Liposome Delivery Vehicle Comprising Twelve Amino AcidSegment of the γ Subunit of Fibrinogen

This Example pertains to the preparation of liposomes that areconjugated to the dodecapeptide HHLGGAKQAGDV (SEQ ID NO: 16), a segmentof the y subunit of fibrinogen, to achieve site-specific binding toirradiated tumors.

In initial experiments,1,1-Dioctadecyl-3,3,3′,3′-tetramethylindocarbo-cyanine perchlorate(DiI), a lipid fluorescent marker, was added to liposome-fibrinogenconjugates and injected by tail vein. As a control, liposomes withoutfibrinogen conjugation were injected. These produced no increase influorescence in irradiated tumors. Fluorescence within blood vessels oftumors treated with ionizing radiation was observed for theliposome-fibrinogen conjugates. These findings support site-directeddrug delivery to the fibrinogen receptor in irradiated tumors.

Cationic liposomes can be conjugated to antibodies and peptides(Kirpotin et al., 1997); however, these liposomes bind to lipophilicproteins in the serum, which reduces the circulation time. Therefore,polyethylene glycol (PEG) is used to coat the drug delivery systems. PEGprolongs circulation time (Nam et al., 1999; Koning et al., 1999).

In this Example, HHLGGAKQAGDV (SEQ ID NO: 16) is conjugated to liposomesand encapsulated by PEG. It is then determined whether both large MWtherapeutic proteins and small MW cytotoxic compounds can be localizedto irradiated tumors by liposomes conjugated to HHLGGAKQAGDV (SEQ ID NO:16). The linking peptide SGSGS (SEQ ID NO: 31) is placed at theC-terminus, which is linked to liposomes. Liposomes are conjugated tothe SH on Cys at the C-terminus. The biodistribution ofHHLGGAKQAGDV-SGSGSC (SEQ ID NO: 29)-liposome is studied and the lengthof the linking peptide is altered as necessary. In the event that PEGwill not achieve membrane fusion that is comparable to cationicliposomes, the length of the linking peptide is also altered asnecessary.

Preparation of HHLGGAKQAGDV (SEQ ID NO: 16)—Long Circulatory Liposomes.Two methods of conjugating liposomes to peptides are employed. The firstmethod conjugates the liposome to the N-terminus, and thus the linkingpeptide is placed at the N-terminus. This method arranges the conjugatein the following configuration: liposome-SGSGS-HHLGGAKQAGDVC (SEQ ID NO:27). The second method conjugates the liposome to the C-terminus of thepeptide. This method is facilitated by placing a Cys residue at theC-terminus. This method arranges the conjugate into the configuration:HHLGGAKQAGDV-SGSGSC (SEQ ID NO: 29)-liposome. These two methods providealternatives in the event that one configuration is useful forsite-specific drug delivery over the other configuration. These methodsare also applicable to larger polypeptides and proteins, includingfibrinogen itself.

Method 1

Step (1) Synthesis of Maleimide-PGE-PE

The lipophilic SH reactive reagent with a long spacing arm issynthesized from maleimide-PEG 2000-NHS ester (Prochem, High Point,N.C., United States of America), dioleoylphosphatidylethanolanime (DOPE,Avanti Polar Lipids, inc., Alabaster, Ala., United States of America),and triethylamine in chloroform (1:1:1.5). Resulting maleimide-PEG2000-DOPE is purified by flash column.

Step (2) Preparation of Thiolated HHLGGAKQAGDV (SEQ ID NO: 16)

Under stirring, to a solution of HHLGGAKQAGDV (SEQ ID NO: 16; 2 mg/mL)in 0.01 M HEPES 0.15 M NaCl buffer pH 7.9, containing 10 mM EDTA and0.08% sodium azide, is added in five-fold excess of freshly preparedTraut's Reagent in the same buffer. Reaction is performed for 30 minutesat 0° C. Thiolated HHLGGAKQAGDV (SEQ ID NO: 16) is then purified using adesalting PD-10 column (Amersham Biosciences).

Preparation of Maleimide-Containing Long Circulating Liposomes withfluorescent labels. PGE 2000-PE, cholesterol, Dipalmitoyl phosphocholine(Avanti Polar Lipids), DiI, and maleimide-PEG-2000-DOPE is dissolved inchloroform and mixed at a ratio of 10:43:43:2:2 in a round bottom flaskas described in Leserman, 1980. The organic solvent is removed byevaporation followed by desiccation under vacuum for 2 hours. Liposomesare prepared by hydrating the dried lipid film in PBS at a lipidconcentration of 10 mM. The suspension is then sonicated 3×5 minutesuntil clear, forming unilamellar liposomes of 100 nM in diameter.

Conjugation of thiolated HHLGGAKQAGDV (SEQ ID NO: 16) to maleimidecontaining liposomes. Prepared vesicles and thiolated protein is mixedin 10 mm HEPES, 0.15 M NaCl, and EDTA pH 6.5. The final concentrationsfor proteins and liposomes are 0.25 g/L and 2.5 mM, respectively. Themixture is incubated for 18 hours at room temperature and vesicles areseparated from unconjugated protein by gel filtration on a SEPHAROSE®4B-CL column (Amersham Biosciences).

Method 2

To conjugate the peptide to long-circulating liposomes, a peptide with aCys residue on the C-terminal is synthesized (PeptidoGenic Research &Co., Livermore, Calif., United States of America). A bifunctional PEG(molecular weight 2000) with a maleic group on one end and NHS group onthe other end is used to conjugate to the aminal group of dioleyolphosphatidyl ethanolamine (DOPE). The resulting maleic-PEG-DOPE servesas a sulfhydryl-reactive lipid anchor with a peptide linker between thelipid portion and the SH-reactive group. Long-circulating liposomes areprepared by reverse phase evaporation method using a lipid mixturecomposed of DOPC:Cholesterol:PEG-DOPE:maleic-PEG-DOPE:Cy3-DOPE at aratio of 45:44:5:2:2 (molar ratio). The peptide is then conjugated tothe liposomes at pH 7.0 under inert gas for 24 hours at roomtemperature. After the conjugation, the excess of peptide is removedthough a gel filtration step using SEPHACRYL™-100 column with PBS aseluent. The percentage of conjugation of the peptide to the liposomes isestimated by the reduction of free peptide peak.

Experimental Design. HHLGGAKQAGDV (SEQ ID NO: 16) is conjugated toliposomes using SH-reactive group as described above. Liposomes arelabeled with gamma emitters and fluorochromes so that thepharmacokinetics and biodistribution can be measured.HHLGGAKQAGDV-SGSGSC (SEQ ID NO: 29)-Liposomes are then coated with PEGas described above. Tumors are implanted and irradiated as describedabove. HHLGGAKQAGDV (SEQ ID NO: 16)-conjugated encapsulated drugs arethen injected by tail vein injection.

Biodistribution is studied by use of gamma emitters and gamma cameraimaging. Both large molecular weight proteins and small molecular weightcompounds (i.e. active agents) are radiolabeled. A therapeutic protein,tumor necrosis factor is labeled with ¹³¹I by use of IODO-GEN® reagentas described above. ¹³¹I-TNF is encapsulated in liposomes-HHLGGAKQAGDV(SEQ ID NO: 16) conjugates and PEG administered by tail vein asdescribed above.

Doxorubicin is used to study the biodistribution of a small MW compoundthat interacts with radiation. Doxorubicin is encapsulated influorescent liposomes (Avanti Polar Lipids) and PEG-HHLGGAKQAGDV (SEQ IDNO: 16) conjugates and administered by tail vein as described above.Methods of preparing fluorescent liposomes and conjugation ofHHLGGAKQAGDV (SEQ ID NO: 16) to liposomes are described above,Doxorubicin levels in serum and tumors in the Pharmacokinetic core labat Vanderbilt University using standard techniques. Fluorescencemicroscopy is used to measure liposomes in tumors using fluorescencequantification techniques described in Hallahan, 1997a.

Positive control groups. ¹³¹I-labeled HHLGGAKQAGDV-SGSGS-YYYYY (SEQ IDNO: 28) is administered to one group of irradiated tumor bearing miceand compared to biodistribution of encapsulated radiolabeled liposome.These mice are randomly assigned into groups during the same experimentas radiolabeled drugs. Radiolabeled drug binding in each group isquantified and compared to the ¹³¹I-labeled HHLGGAKQAGDV-SGSGS-YYYYY(SEQ ID NO: 28) positive control group.

Negative control groups: Firstly, control tumors are implanted in theleft hind limb of all mice and remain unirradiated. Secondly,SGSGSSGSGSGS-SGSGS (SEQ ID NO: 34) are conjugated to PEG and liposomesand administered to tumor bearing mice following irradiation to verifythat encapsulated drug binding to irradiated tumors is not a generalizedphenomenon. Eight tumor-bearing mice are randomly assigned into each ofthe experimental and control groups. Statistical considerations aredescribed above.

Example 17 Anti-P-selectin scFv Binding to Microvasculature ofIrradiated Cancer

To determine whether anti-P-selectin scFv antibodies bind to irradiatedmicrovasculature, the binding of four antibodies (4A, 12F, 5H, and 10A)was studied using immunofluoresence microscopy. Human head and necksquamous cell carcinoma (HNSCC) cell lines were implanted into the hindlimb of nude mice and grown to 10 mm diameter as in Example 5 (see alsoHallahan et al., 1995b; Hallahan et al., 1998; Hallahan & Virudachalam,1999). Tumors were irradiated and dissected 5 hours later. Dissectedtumors were snap frozen and cryosectioned. Immunofluoresence microscopyof each of the scFv antibodies to human P-selectin demonstrated that theantigen in these tumor sections was expressed by host (mouse) cells,indicating that these epitopes are conserved across species. Each of thescFv antibodies bound to the microvasculature of irradiated HNSCC, butnot to untreated controls.

Example 18 Direct Application of Library to Irradiated Tumors andEndothelial Cells

To study the feasibility of selecting antibodies that bind irradiatedendothelial cells, primary culture human umbilical vein endothelialcells (HUVEC) were used. Negative selection of phage was first performedby removing all phage antibodies that bind within an intact umbilicalvein and to unirradiated endothelium from pooled donors. Unbound phagewere then incubated with HUVEC at 5 hours after irradiation with 2 Gy.Antibodies were prioritized by fluorometric microvolume assay technologywith an FMAT™ 8100 device (PE Biosystems, Foster City, Calif., UnitedStates of America) using irradiated HUVEC in microwells. Selected werescFv antibodies that bind with high affinity to irradiated HUVEC but donot bind to untreated HUVEC. Immunofluorescence microscopy of antibodiesdeveloped to irradiated HUVEC showed that several antibodies did notbind to untreated control cells but did bind to irradiated HUVEC. Thesephage-displayed antibodies were not displaced by anti-P-selectinantibodies indicating that they likely bound to distinctradiation-induced epitopes on HUVEC. A determination of which of theseantibodies binds to human cancer microvasculature is presented inExample 21.

Phage antibodies that bind to irradiated HUVEC and fibroblasts using ahuman Fab antibody 17 library are also selected. Enriched antibodies areprioritized and studied on biopsy specimens from irradiated HNSCCpatients. Antibodies that bind to human tumor blood vessels are isolatedand the radiation-induced antigen(s) to which they bind arecharacterized. See Chang et al., 1991; Garrard et al., 1991; Hoogenboomet al., 1991; Kang et al., 1991; U.S. Pat. No. 5,837,500.

Example 19 In Vivo Testing of scFv Antibody Binding

Several scFv antibodies developed to P-selectin and to α_(2b)β₃ areprioritized by ELISA, BIACORE®, and fluorometric microvolume assaytechnology (the latter using a FMAT® 8100 device from PE Biosystems,Foster City, Calif., United States of America). These antibodies aretested to determine which bind to the greatest percentage of tumorspecimens from irradiated patients, while not binding to biopsies ofskin and mucosa. Biopsy specimens are sectioned on the day of antibodystaining, which is performed as described (Schueneman et al., 2003).Briefly, sections are first incubated with blocking buffer and washed.Fluorescence labeled scFv and Fab antibodies are then incubated with thesections under conditions sufficient to allow binding of the antibodiesto targets. Antibody staining of tumor blood vessels is compared to thatof skin and mucosa biopsies from the same patients. Biopsies frompatients are stained for each of the prioritized antibodies by use offluorescence microscopy and image analysis software as has beendescribed (Geng et al., 2001; Hallahan et al., 2002). Vascular densityis also analyzed simultaneously.

HNSCC xenografts are implanted subcutaneously in the hind limb asdescribed in Hallahan et al., 2003. Antibodies and immunoconjugates withoptimal binding are radiolabeled and injected by tail vein afterirradiation of xenografts. The tumor bearing hind limb is irradiatedwith 0 Gy (Control), or daily fractionated radiation (2 Gy×7) asdescribed in Schueneman et al., 2003 and Hallahan et al., 2003.

Example 20 Mass Spectrometry Analysis of scFv Antibodies

To develop a high-throughput screening technique for phage libraryantibodies targeted to radiation-induced neoantigens (for example,P-selectin or α_(2b)β₃ integrin) and measure tumor specificity of scFvantibodies developed from phage antibody libraries, a largephage-displayed scFv recombinant antibody library was developed. Thephage library was incubated with purified P-selectin protein, andhigh-affinity phage antibody clones were recovered by washing at pH 1.The antibody clones were assayed for antigen-binding activity by ELISA.The clones producing antibodies reactive with P-selectin were grown andinduced to express P-selectin-specific scFv antibodies on a large scale.

The phage antibody library was also screened for scFv that bound toexpired human platelets obtained from blood banks. Phage that werenonspecifically bound to inactivated platelets were first subtractedfrom the library. Platelets were activated to induce α_(2b)β₃ integrinin the active conformation. Bound phage were displaced by the additionof a monoclonal antibody specific for α_(2b). The displaced phage wererecovered and used to produce α_(2b) antibodies.

P-selectin and α_(2b) scFv antibodies were individually spotted inmatrix and evaluated by mass spectrometry for size to determine sets of6 that can be effectively discriminated by mass spectrometry based upondifferences in their molecular weights (approximately 400 mass unit sizedifference). Antibodies to P-selectin and to α_(2b) were administered insets of 6 by tail vein injection into mice bearing irradiated tumors.The tumors were dissected and antibody binding was measured by MALDI-TOFmass spectrometry.

Soluble rodent scFv antibodies to P-selectin and to α_(2b) weredeveloped, several of which were definitively measured in matrix byMALDI-TOF mass spectrometry. Of these, 9 soluble rodent scFv antibodiesto P-selectin and 9 soluble rodent scFv antibodies to α_(2b) weredifferentially detected in sets of 3 in mice tumors via MALDI-TOF massspectrometry. Spectrum analysis allowed quantification of the amount ofthe individual antibodies binding within the tumors.

Example 21 Binding of scFv to Human Cancer Microvasculature

Using the methods and procedures described hereinabove, scFv antibodiesthat are found to bind to HUVEC cells are tested for binding to humancancer microvasculature either in vivo or in vitro on biopsy samples.

Negative selection of the entire phage library (2×10⁹) is firstperformed on untreated vascular endothelium and platelets.Phage-displayed antibodies that bind to normal endothelium and plateletsare discarded, while phage that do not bind are used for high throughputscreening as follows.

HUVEC cells are grown to confluence in complete medium and human serumin 1536-well plates. Cells are irradiated with 3 Gy. Those scFv phageantibodies that bind to the isolated, irradiated endothelium areselected by use of an automated colony picker, followed by highthroughput screening using an FMAT® device (PE Biosystems, Inc., FosterCity, Calif., United States of America), which is used to quantifyfluorescence-labeled phage localized and concentrated on the irradiatedendothelial cell surface.

Example 22 Laser Capture Microdissection

Microvasculature is identified during laser capture microdissection(LCM). The use of an LCM system allows selected single cells or groupsof cells to be analyzed. LCM is used to dissect the vascular endotheliumand luminal proteins from a frozen section of an irradiated tumor. Thephage antibody library is added to these blood vessels and scFv phageantibodies that are recovered from the irradiated tumor vasculature areselected using an automated colony picker. Phage undergo several roundsof selection to reduce nonspecific binding. Identified antibodies arefurther selected using FMAT.

Example 23 Antibodies to TIP-1

A two hybrid system identified the Tax-interacting protein-1 (TIP-1) asa putative receptor for the recombinant HGDPNHVGGSSV (SEQ ID NO: 71)peptide. Antibodies (monoclonal and antiserum) have been developed toTIP-1. FIG. 2 presents data with respect to the binding of an exemplaryscFV antibody binding to TIP-1. This antibody also blocked HGDPNHVGGSSV(SEQ ID NO: 71) peptide binding to irradiated tumors.

Example 24 TIP-1 Expression in Control and Irradiated Tumors

TIP-1 expression was studied in irradiated tumors. FIGS. 3A and 3B showsimmunohistochemical staining of TIP-1 in control and irradiated tumors(3 Gy), respectively. This study showed that TIP-1 expression increasedin the vascular endothelium of irradiated tumors. FIG. 3A shows littleor no TIP-1 was expressed in untreated tumors. FIG. 3B shows increasedimmunohistochemical staining of TIP-1 in tumors at 6 hours aftertreatment with 3 Gy. Tumor microvasculature showed little or no TIP-1expression in unirradiated tumor vascular endothelium, as compared torobust staining of TIP-1 protein in the endothelium at 4 hours afterirradiation of tumors.

Western immunoblots were used to quantify TIP-1 expression in tumors.Studies were performed using polyclonal antibody. FIG. 4 shows theWestern immunoblot of protein extracted from control and irradiatedtumors. In this experiment, cell membrane proteins were separated fromcytoplasmic proteins to determine whether TIP-1 is expressed at the cellsurface. Cell surface expression of TIP-1 could be required for phagepeptides to bind within tumors following injection of the phage into thecirculation. FIG. _E shows increased TIP-1 expression in cell membranepreparation in response to radiation. These data support the hypothesisthat TIP-1 is a putative receptor for HGDPNHVGGSSV (SEQ ID NO: 71)ligand binding to irradiated tumors.

To further test this hypothesis, experiments studying TIP-1 blockingantibodies are done. Affinity purification experiments to test thehypothesis that multiple PDZ containing receptors bind HGDPNHVGGSSV (SEQID NO: 71) in irradiated tumors are also done.

Example 25 Biodistribution and Pharmacokinetics of Recovered Phage

To determine the feasibility of imaging the biodistribution of phagedisplayed peptides, near infrared (NIR) imaging of Cy7 labeled peptidesthat were recovered from irradiated tumors was employed. Tumor specificbinding and pharmacokinetics of each of these phage peptides was tested.Some of the phage that were recovered from irradiated tumors werecompared in order to determine which peptide has the greatest tumorspecific binding. Phage were first labeled with Cy7 to allow imaging byuse of NIR imaging (Xenogen) within the Vanderbilt Small Animal ImagingCore Lab. Tumors were implanted into both hind limbs of nude mice andthe right hind limb tumor was irradiated with 3 Gy. The left hind limbtumor served as an internal negative control. Cy7-labeled phage wereinjected into the venous circulation by use of the jugular catheter. Thebiodistribution of Cy7 labeled phage was then imaged by NIR imaging eachday for a total of nine days.

FIGS. 5 and 6 show the NIR imaging of Cy7 labeled phage. Phage showedtumor binding at 24 hours after irradiation. FIG. 7 is a bar graphindicating that percentage of total phage localized to the tumorfollowing clearance from the circulation. Although several phagepeptides show selective binding within the tumor, the HGDPNHVGGSSV (SEQID NO: 71) phage shows very highly selective binding to irradiatedtumors.

The pharmacokinetics of the HGDPNHVGGSSV (SEQ ID NO: 71) phage was alsocompared to that of the RGDGSSV (SEQ ID NO: 75), HGSSV (SEQ ID NO: 76)and other phage. The HGDPNHVGGSSV (SEQ ID NO: 71) phage was unique inthat it demonstrated tumor specific binding for nine days. FIG. 8 showsthe daily NIR imaging of Cy7 labeled HGDPNHVGGSSV (SEQ ID NO: 71). Onday one, the phage peptide circulates throughout the entire body. By daythree, the labeled phage was cleared from the circulation through thekidney and collected in the bladder. Tumor binding was the only siteother than the kidney on days 3 through 7. Thereafter, tumor specificbinding was sustained.

FIG. 9 compares the kinetics of tumor binding by HGDPNHVGGSSV (SEQ IDNO: 71) phage to that of the RGDGGSSV (SEQ ID NO: 75) phage. Theintensity of NIR images was measured in each pixel. NIR intensity intumor and the rest of the body was tabulated as the percentage of totalNIR emission. Immediately after injection, Cy7 labeled phage wasdistributed throughout the entire body (day 0). By day one, binding intumor was detected and clearance from the circulation occurred throughthe kidney. The percentage of HGDPNHVGGSSV (SEQ ID NO: 71) binding intumor continued to increase, while the distribution of this phagethroughout the rest of the body cleared. By day seven, 90% of the phagewas bound within the tumor and tumor specific binding was sustainedbeyond nine days. In comparison, the RGOGGSSV (SEQ ID NO: 75) phageachieved 55% binding at day two, but cleared from both tumor and body byday four. HGDPNHVGGSSV (SEQ ID NO: 71), therefore, has greater tumorspecific binding and prolonged pharmacokinetics as compared to the nextbest phage, RGDGGSSV (SEQ ID NO: 76).

Example 26 Histologic Site of Phage Binding

To determine the histologic pattern of phage binding, tumors were fixedat 4 hours and 7 days after irradiation and phage injection. Sectionswere stained using the anti-phage antibody and counter-stained with H &E. FIG. 10 shows staining of the anti-phage antibody (brown). TheHGDPNHVGGSSV (SEQ ID NO: 71) phage was localized at the vascularendothelium as compared to the RGDGGSSV (SEQ ID NO: 76) phage, whichbinds within the lumen of blood vessels (FIG. 10B). Negative controlphage (the phage vector without insert) showed no binding withinirradiated tumors. These findings indicated that HGDPNHVGGSSV (SEQ IDNO: 71) can be binding to a radiation-inducible molecule in tumorendothelium. Moreover, the HGDPNHVGGSSV (SEQ ID NO: 71) phagesubsequently traversed the vascular endothelium and bound to cancercells (FIG. 10D).

Example 27 Fluorescence-Labeled HGDPNHVGGSSV (SEQ ID NO: 71)

To determine the feasibility of using this peptide to recover theputative receptor, HGDPNHVGGSSV (SEQ ID NO: 71) binding was studied intumor vasculature and endothelial cells in culture. HGDPNHVGGSSV (SEQ IDNO: 71) peptide was injected into the circulation of mice bearingirradiated tumors (3 Gy). HGDPNHVGGSSV (SEQ ID NO: 71) was first labeledwith Texas red. Tumors were sectioned and counter stained with eosin.FIG. 11 shows that the Texas red conjugated HGDPNHVGGSSV (SEQ ID NO: 71)peptide maintained the ability to bind to tumor microvasculaturefollowing irradiation. Fluorescence-labeled HGDPNHVGGSSV (SEQ ID NO: 71)bound to tumor microvasculature treated with 3 Gy (FIG. 11A), but not tountreated vessels. NIR imaging of Cy7-labeled HGDPNHVGGSSV (SEQ ID NO:71) is shown in the mouse image (FIG. 11A).

Example 28 Tumor Targeting with a TIP-1 Binding Peptide

To determine whether peptide conjugated to nanoparticle can be used totarget therapy to cancer, the HGDPNHVGGSSV (SEQ 16 NO: 71) peptide wasattached to a polyglycine linker and attached to a protein core by useof biotin. Streptavidin was then labeled with Cy7 to allow imaging oftreated animals. FIG. 12 shows that the labeled Streptavidin-peptidecomplex bound within treated tumors but not untreated control tumors onthe left. This system allows determination of whether peptide conjugatesachieve the same level of binding as the phage displayed peptide shownin FIG. 6.

Orthopotic tumors have been studied in order to verify that peptidebinding in treated tumors is not limited to subcutaneous implantation.FIG. 13 shows peptide binding in the glioblastoma within the brains oftreated mouse and in the H460 lung cancer in the thorax of the treatedmouse. FIG. 13C shows peptide binding within the treated coloncarcinoma. FIG. 14 shows peptide binding in 2 different orthotopicprostate tumors. These studies showed that all tumor types and allorthotopic tumor models demonstrated binding of the HGDPNHVGGSSV peptidefollowing treatment with radiation.

Example 29 HGDPNHVGGSSV (SEQ ID NO: 71) does not Bind to IrradiatedNormal Tissue

To determine whether HGDPNHVGGSSV (SEQ ID NO: 71) peptide binds tonormal tissues, mice treated with 3 Gy to normal tissue, followed bytail vein injection of Cy7-labeled Streptavidin-HGDPNHVGGSSV (SEQ ID NO:71), were imaged. FIG. 14C shows peptide binding to the abdominal coloncancer and no binding in the irradiated liver (red arrow) and nogastrointestinal binding. FIG. 15 shows binding in the prostate tumorbut no binding within the rest of the abdomen following irradiation ofabdominal organs.

Example 30 Orthotopic Prostate Cancer Models

Two orthotopic tumor models within the prostates of mice are studied.The PC3 injection into the prostate of nude mice develops over 2 weeks(see FIGS. 14A and 14B). A colony of the prostate-specific conditionalPTEN transgenic mice, which develop tumors within 20-24 weeks (see FIG.14C), is also available. Tumors were monitored by ultrasound and PSAlevels as described in Yankeelov et al., 2006. FIG. 14 shows NIR imagingof labeled-HGDPNHVGGSSV (SEQ ID NO: 71) binding in irradiated (3 Gy)orthotopic prostate cancers following injection through jugularcatheters. FIG. 14B shows the negative control peptide with no bindingin irradiated PC3 orthotopic tumor (FIG. 14). FIG. 15 shows the PC3tumor within the prostate during laparotomy of the euthanized mouseimaged in FIG. 14A. The arrow indicates the lobolated tumor in thepelvis. NIR was also used to image each of the organs (FIG. 15B).Labeled peptide in the prostate tumor was >20-fold higher than anyorgan. FIG. 16 shows the transgenic prostate tumor in the pelvis of theeuthanized mouse imaged in FIG. 14C. NIR was also used to image each ofthe organs (FIG. 16B). Labeled peptide in the prostate tumorwas >20-fold higher than any organ. These data show that HGDPNHVGGSSV(SEQ ID NO: 71) bound to the orthotopic prostate tumors.

Example 31 HVGGSSV (SEQ ID NO: 35) Conjugates Bind Endothelial Cells

To determine the fate of the HGDPNHVGGSSV (SEQ ID NO: 71) peptide afterbinding to vascular endothelium, fluorescently labeled Streptavidinconjugated to HGDPNHVGGSSV (SEQ ID NO: 71) was employed peptide.Endothelial cells were irradiated and the fluorescent confocalmicroscopy was used to image HGDPNHVGGSSV (SEQ ID NO: 71)-Streptavidinin endothelial cells (see FIG. 16). The fluorescent-labeled HGDPNHVGGSSVpeptide did not bind to untreated endothelial cells (FIG. 16A). Peptidebinds to the surface of endothelial cells within four hours ofirradiation (panel 16B). In comparison, peptide was then allowed toincubate on endothelial cells overnight. Panel 16C shows theinternalized HGDPNHVGGSSV peptide adjacent to the nucleus of irradiatedvascular endothelium. These results support that the HGDPNHVGGSSVpeptide will facilitate internalization of gene therapy vectors.

REFERENCES

All references listed in the instant disclosure, including but notlimited to all patents, patent applications, scientific journals, andGENBANK® database entries (including all annotations available therein)are incorporated herein by reference in their entireties to the extentthat they supplement, explain, provide a background for or teachmethodology, techniques and/or compositions employed herein.

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It will be understood that various details of the presently disclosedsubject matter can be changed without departing from the scope of thepresent disclosure. Furthermore, the foregoing description is for thepurpose of illustration only, and not for the purpose of limitation.

1-57. (canceled)
 58. A method for detecting a tumor in a subject, themethod comprising: (a) exposing a target area of the subject where thepresence of a tumor is suspected to ionizing radiation; (b)administering to the subject a composition to detect the presence ofTIP-1 in the target area, wherein the composition comprises one or moretargeting antibodies, wherein each targeting antibody i. is capable ofbinding to a TIP-1 polypeptide expressed by an irradiated tumor, and ii.is conjugated to a detectable label, and iii. substantially lacksbinding to a control tissue; and (c) detecting the detectable label todetect the presence of TIP-1, wherein the presence of TIP-1 indicatesthe presence of a tumor in the target area of the subject.
 59. Themethod of claim 58, wherein the antibody that binds to a TIP-1polypeptide is selected from the group consisting of a polyclonalantibody, a monoclonal antibody, a scFv antibody, and an antibodyfragment that binds to a TIP-1 polypeptide.
 60. The method of claim 59,wherein the antibody is humanized.
 61. The method of claim 58, whereinthe exposing comprises exposing the tumor to less than about 2 Gyionizing radiation.
 62. The method of claim 61, wherein the exposingcomprises exposing the tumor to at least about 2 Gy ionizing radiation.63. The method of claim 62, wherein the exposing comprises exposing thetumor to about 10 Gy to about 20 Gy ionizing radiation.
 64. The methodof claim 58, wherein the administering comprises administering thetargeting antibody by intravascular provision.
 65. The method of claim58, wherein the administering comprises administering the targetingantibody subsequent to radiation exposure.
 66. The method of claim 65,wherein the administering comprises administering the targeting antibody0 hours to about 24 hours following radiation exposure.
 67. The methodof claim 66, wherein the administering comprises administering thetargeting antibody about 4 hours to about 24 hours following radiationexposure.
 68. The method of claim 58, wherein the subject is awarm-blooded vertebrate.
 69. The method of claim 58, wherein thedetecting comprises detecting the radionuclide label using positronemission tomography, single photon emission computed tomography, gammacamera imaging, or rectilinear scanning.
 70. The method of claim 58,wherein the tumor comprises a tumor selected from the group consistingof bladder carcinoma, breast carcinoma, cervical carcinoma,cholangiocarcinoma, colorectal carcinoma, gastric sarcoma, glioma, lungcarcinoma, lymphoma, melanoma, multiple myeloma, osteosarcoma, ovariancarcinoma, pancreatic carcinoma, prostate carcinoma, stomach carcinoma,a head, a neck tumor, and a solid tumor.
 71. The method of claim 70,wherein the tumor is selected from the group consisting of a glioma, amelanoma, a lung carcinoma, and a prostate carcinoma.
 72. The method ofclaim 58, further comprising simultaneously detecting two or more tumorsin the subject.
 73. The method of claim 72, wherein the two or moretumors in a subject comprise two or more tumor types.